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CMTM6 / CKLF-like MARVEL transmembrane domain-containing protein 6 · IHC design guide
Design Immunohistochemistry for CMTM6
Plan chromogenic CMTM6 IHC on paraffin sections using the cytoplasmic tissue profile (HPA tissue IHC). Select high-staining Purkinje or endometrial glandular cells (HPA tissue IHC), and start the catalog antibody at 1:100–1:300 (datasheet).
Evidence assembled Oct 2026 · For research use; verify linked source records and product datasheet before use
CMTM6 Immunohistochemistry Experimental Design Guide
Expected localisation, validated protocols, controls and antibodies — the at-a-glance facts below, then the full design guide.
Must know before staining
| Expected localisation | Cytoplasmic tissue staining (HPA tissue IHC); membrane and endosomes (UniProt) | |
| Staining pattern | Cytoplasmic staining in most tissues (HPA tissue IHC) | |
| Antigen retrieval | Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen) | |
| Positive control | Cerebellum+4 more · see all | |
| Negative control | Hippocampus+1 more · see all |
Important caveats
Reasons your staining may differ from the expected pattern.
| Fixation | Keep fixation consistent across sections (standard IHC practice; not target-specific) | |
| Caveat | Antibody staining and RNA show medium consistency (HPA tissue IHC) | |
| Regulation | No CMTM6-specific induction reported (UniProt) | |
| Isoform / epitope | No isoforms listed; epitope side matters across 4 membrane spans (UniProt) |
Section 1
Recommended CMTM6 IHC & IF Protocols
The catalog antibody’s IHC-P protocol is accompanied by published CMTM6 protocols for gastric, hepatocellular and renal carcinomas (PMC7842018; PMC8353897; PMC13039633).
| Sample | Paraffin-embedded human oophoroma tissue; fixative not specified (datasheet A14107) |
| Fixation | Image fixative and duration unreported (datasheet A14107); verify before use. |
| Sectioning | 4–5 µm sections on charged slides (standard) |
| Deparaffinisation | Xylene, graded ethanol series to water (standard) |
| Antigen retrieval | Heat-induced epitope retrieval in citrate buffer, pH 6.0, 20 min at 95–98 °C (standard rule: cytoplasmic / membrane antigen) |
| Peroxidase block | 3% H2O2, 10 min, room temperature (standard) |
| Blocking | 10% normal serum of the secondary host, 30 min, room temperature (standard) |
| Primary antibody | Rabbit anti-CMTM6, 1:100-1:300 (datasheet A14107) |
| Primary incubation | Overnight at 4 °C (standard) |
| Detection | HRP-polymer secondary, DAB chromogen 5–10 min (standard) |
| Counterstain | Hematoxylin, blue, dehydrate and mount (standard) |
| Expected result | CMTM6-positive staining in purkinje cells of cerebellum (HPA tissue IHC: High). HPA tissue profile: Cytoplasmic expression in most tissues. No signal in the no-primary control. |
💡Decision noteStart with citrate pH 6.0 retrieval at 95–98 °C for 20 min (page antigen retrieval); use each paper’s conditions when reproducing its protocol.
Section 2
What Is the Expected CMTM6 Staining Pattern?
CMTM6 is a four-pass membrane protein found at the cell surface and in early and recycling endosomes (UniProt Q9NX76 topology and subcellular location). In tissue IHC, expect predominantly cytoplasmic staining, including strong staining in selected glandular and urothelial cells (HPA: cytoplasmic expression in most tissues; High in endometrial glandular cells and bladder urothelial cells). HPA rates its tissue IHC reliability Enhanced, with medium consistency against RNA expression (HPA: tissue IHC reliability).
| Cytoplasmic staining in endometrial or fallopian tube glandular cells, or bladder urothelial cells. | This fits documented high-staining cell populations (HPA: High in these cells). Vesicular or membrane-associated detail is plausible from the protein's location, but tissue IHC should be judged against HPA's predominantly cytoplasmic pattern (UniProt Q9NX76 subcellular location; HPA: cytoplasmic expression in most tissues). |
| Predominantly nuclear staining with little cytoplasmic signal. | A nuclear-dominant pattern conflicts with the documented membrane and endosomal locations and should prompt a specificity review (UniProt Q9NX76 subcellular location; HPA: cytoplasmic expression in most tissues). Review the counterstain and compare the primary-antibody result with a suitable negative control (standard IHC practice). |
| Strong signal in hippocampal glial cells or skeletal-muscle myocytes. | These cell populations are reported as not detected, so conspicuous staining raises concern about cross-reactivity or endogenous detection activity (HPA: Not detected in hippocampal glial cells and skeletal-muscle myocytes; standard IHC practice). Check the signal's compartment and run detection controls before assigning it to CMTM6 (standard IHC practice). |
| Diffuse color across cells, stroma, and slide background without a defined cellular pattern. | This is difficult to interpret as the documented predominantly cytoplasmic signal (HPA: tissue IHC profile). Nonspecific antibody binding, incomplete blocking, or residual detection reagents are general IHC possibilities; assess a no-primary control and background distribution (standard IHC practice). |
| No convincing signal in an expected high-staining cell population. | Absence of signal in endometrial glandular or bladder urothelial cells conflicts with the HPA observations, though an individual section still needs adequate tissue and interpretable controls (HPA: High in these cells; standard IHC practice). Recheck the IHC workflow before interpreting the result as biological absence (standard IHC practice). |
💡Expected CMTM6 appearanceCall the stain positive when defined, predominantly cytoplasmic signal appears in an HPA high-staining population such as bladder urothelial cells; nuclear-dominant or indiscriminate background color is suspect (HPA: cytoplasmic expression in most tissues; High in bladder urothelial cells; UniProt Q9NX76 subcellular location; standard IHC practice).
| Membrane topology and compartment | CMTM6 has four transmembrane segments and cytoplasmic and extracellular loops (UniProt Q9NX76 topology). Its cell-surface and endosomal locations support membrane-associated and vesicular interpretation, while HPA describes tissue IHC broadly as cytoplasmic (UniProt Q9NX76 subcellular location; HPA: tissue IHC profile). |
| Cell-type baseline | High staining is reported in Purkinje, selected glandular, and bladder urothelial cells; glial cells in hippocampus and skeletal-muscle myocytes are not detected (HPA: tissue IHC levels). Select controls by the recorded cell population, since a tissue can contain several cell types (standard IHC practice). |
| Strength of tissue evidence | HPA labels tissue IHC reliability Enhanced, while reporting medium consistency between staining and RNA expression (HPA: tissue IHC reliability). This supports using its pattern as a reference without treating every unexpected cell-level result as settled by the summary alone (standard IHC interpretation). |
| IF/ICC Q: where should CMTM6 appear? | A: Mainly in vesicles, with Vesicles listed as an approved main location; HPA shows ICC-IF images in RT-4, U-251MG, and U2OS (HPA: subcellular ICC-IF). That cell-image result complements the tissue IHC profile but does not set an IHC scoring threshold (HPA: tissue IHC profile; standard IHC interpretation). |
| Situation | Likely cause | Next action |
|---|---|---|
| Expected high-staining cells are blank. | The tissue may lack intact target cells, or a general IHC workflow step may have failed (HPA: High in endometrial glandular and bladder urothelial cells; standard IHC practice). | Confirm cell identity and tissue integrity, then review the documented IHC-P conditions, retrieval, primary incubation, and detection controls (standard IHC practice). CMTM6-specific fixation sensitivity is unreported in the supplied sources. |
| The whole section has diffuse chromogen or high background. | Nonspecific binding or detection-system background can obscure cellular localisation (standard IHC practice). | Inspect a no-primary control; check blocking, washes, and detection reagents, then reassess whether a defined cytoplasmic pattern remains (standard IHC practice; HPA: tissue IHC profile). |
| Nuclei dominate the apparent positive signal. | The pattern conflicts with CMTM6's documented membrane and endosomal locations and HPA's cytoplasmic tissue profile (UniProt Q9NX76 subcellular location; HPA: tissue IHC profile). | Compare with the counterstain and negative controls, and repeat the specificity assessment before scoring nuclei as positive (standard IHC practice). |
| A nominally negative cell population stains strongly. | Cross-reactivity or endogenous detection activity is possible when staining appears in HPA not-detected populations (HPA: hippocampal glial cells and skeletal-muscle myocytes; standard IHC practice). | Verify the cell type, compare compartment and intensity with an HPA high-staining control, and inspect the appropriate detection controls (HPA: tissue IHC levels; standard IHC practice). |
| Signal appears only at cell borders or as scattered puncta. | Cell-surface and endosomal locations can yield these appearances, although HPA's tissue IHC summary calls the overall pattern cytoplasmic (UniProt Q9NX76 subcellular location; HPA: tissue IHC profile). | Assess whether the signal belongs to the expected cell population and whether controls are clean; report the observed compartment rather than forcing a uniform cytoplasmic score (HPA: tissue IHC levels; standard IHC practice). |
Experiment evidence
IHC & IF images showing CMTM6 staining
A14107 · IHCImmunohistochemical analysis of paraffin-embedded human-oophoroma, antibody was diluted at 1:100
HPA · Cerebral cortexHuman Protein Atlas IHC, Cerebral cortex. Source: https://www.proteinatlas.org/ENSG00000091317-CMTM6/tissue/cerebral+cortex#imid_6838768
HPA · ColonHuman Protein Atlas IHC, Colon. Source: https://www.proteinatlas.org/ENSG00000091317-CMTM6/tissue/colon#imid_6838694
HPA · LiverHuman Protein Atlas IHC, Liver. Source: https://www.proteinatlas.org/ENSG00000091317-CMTM6/tissue/liver#imid_6838687
HPA · KidneyHuman Protein Atlas IHC, Kidney. Source: https://www.proteinatlas.org/ENSG00000091317-CMTM6/tissue/kidney#imid_6838680
HPA · ICC-IF RT-4Human Protein Atlas immunofluorescence, RT-4, antibody HPA063491; green = CMTM6, blue = nucleus, red = microtubules.
HPA · ICC-IF RT-4Human Protein Atlas immunofluorescence, RT-4, antibody HPA063491; green = CMTM6, blue = nucleus, red = microtubules.
← swipe / scroll for more images →
Real IHC / IF data behind the staining-pattern expectations in this section.
Sample controls for CMTM6 IHC & IF
🧪Run urinary bladder first: urothelial cells should stain (HPA: High in urothelial cells). Run skeletal muscle as a negative tissue (HPA: Not detected in myocytes); nuclei on the bladder slide should lack specific signal because CMTM6 localizes to membranes and endosomes (UniProt Q9NX76 subcellular localization).
Positive control tissue: Cerebellum (Purkinje cells, HPA High)
Negative control tissue: Hippocampus (HPA Not detected)
ICC-IF cell lines (HPA subcellular resource): HPA ICC-IF images show CMTM6 in RT-4, U-251MG, U2OS, with annotated localisation: Vesicles (approved) (HPA subcellular).
Technical controls: Include no-primary or secondary-only and host- and immunoglobulin-class-matched isotype controls, plus a CMTM6 knockout sample as a biological negative (standard IHC practice). Quench endogenous peroxidase before chromogenic detection, particularly where the bladder section contains blood cells (standard IHC practice).
⚠️Feasibility: A target-specific fixation window and retrieval dependency are unreported in the supplied evidence; optimize antigen retrieval empirically (supplied target/application evidence; standard IHC practice). The selected A14107 paraffin-section caption reports 1:100 dilution but does not state the fixative (A14107 tissue-IHC caption). Frozen sections are not established as easier here; ICC-IF images in RT-4, U-251MG and U2OS show mainly vesicular localization, but do not establish performance in frozen tissue (HPA: subcellular).
HPA tissue IHC evidence for CMTM6
Comprehensive Human Protein Atlas IHC scoring per tissue (reliability: Enhanced — Medium consistency between antibody staining and RNA expression data.). Rows are taken directly from the HPA tissue chart — click any row's HPA link to view the source.
Positive expression · recommended positive controls
| Tissue | Cell type | Level | Evidence | Source |
|---|---|---|---|---|
| Cerebellum | Purkinje cells | High | Protein (IHC) | HPA → |
| Endometrium | Glandular cells | High | Protein (IHC) | HPA → |
| Fallopian tube | Glandular cells | High | Protein (IHC) | HPA → |
| Rectum | Glandular cells | High | Protein (IHC) | HPA → |
| Urinary bladder | Urothelial cells | High | Protein (IHC) | HPA → |
Section 3
Advanced CMTM6 IHC Tips
Troubleshoot CMTM6 staining in paraffin section chromogenic IHC by checking processing, compartment, controls, and cell specific scoring before interpreting signal.
How should I adjust retrieval when CMTM6 staining is weak?
Use citrate pH 6.0 HIER at 95–98 °C for 20 min (page retrieval setting). Deparaffinize and rehydrate sections completely before heating, then cool and wash them consistently across runs (standard IHC practice). CMTM6 has 4 transmembrane segments and short extracellular loops, but the antibody epitope is unspecified (UniProt Q9NX76 topology; supplied antibody evidence). Compare adjacent sections using a positive control such as endometrial glandular cells (HPA: High), while keeping dilution and detection constant. If signal remains weak, test another buffer or heating duration as a fallback, checking tissue morphology and background alongside signal (standard IHC practice).
Could fixation explain variable CMTM6 staining between paraffin blocks?
Target specific fixation sensitivity is unknown because no CMTM6 fixation experiment or fixative is supplied for this antibody (supplied IHC evidence). The A14107 tissue caption reports paraffin embedded human oophoroma and a 1:100 dilution, but gives no fixative (A14107 tissue IHC caption). Document each block’s actual fixative, fixation duration, and processing history before comparing staining (standard IHC practice). Run sections from those blocks together with the same citrate pH 6.0 retrieval for 20 min (page retrieval setting). If results differ, compare preserved tissue morphology and a shared control before attributing the difference to fixation (standard IHC practice).
Should CMTM6 staining look membranous or cytoplasmic in tissue?
Assess both cell borders and punctate cytoplasmic signal: CMTM6 is assigned to the cell membrane and early and recycling endosome membranes (UniProt Q9NX76 subcellular annotation). Tissue IHC is reported as cytoplasmic in most tissues (HPA: tissue IHC profile), while cell imaging places it mainly in vesicles (HPA: subcellular summary). Diffuse chromogenic staining alone cannot resolve an individual vesicle or establish which membrane contains CMTM6 (standard IHC interpretation). Compare the pattern within the same cell type across well preserved regions and a matched control (standard IHC practice). Record membranous and cytoplasmic staining separately when their proportions differ between specimens (standard IHC scoring practice).
What should I check if antibodies produce different CMTM6 patterns?
First compare each antibody’s documented immunogen and mapped epitope, because epitope information is not supplied for the selected antibody (supplied antibody evidence). The record lists one 183 aa chain and 0 isoforms, so an isoform explanation is unsupported here (UniProt Q9NX76 processing and isoforms). CMTM6 has cytoplasmic segments at residues 1–39, 89–106, and 156–183, plus two short extracellular loops (UniProt Q9NX76 topology). Fixation and retrieval can affect access to epitopes in sections, so compare antibodies on adjacent sections under their validated conditions (standard IHC practice). Require agreement in cell distribution and compartment, with appropriate controls, before combining scores (standard IHC interpretation).
How can I investigate a CMTM6 IHC pattern with multiplex IF?
Use IF or ICC as a separate validation experiment, pairing CMTM6 with a marker that identifies the cell population scored in IHC (standard multiplex IF practice). For example, glandular cells are reported as High in endometrium (HPA: tissue IHC); choose a validated glandular cell marker for that specimen (standard IF practice). Select spectrally separated fluorophores and assign the dimmer channel away from the tissue’s strongest autofluorescence, measured using an unstained control (standard IF practice). Permeabilize for a cytoplasmic epitope, but assess staining without permeabilization when testing access to an extracellular loop; the antibody epitope is unspecified (UniProt Q9NX76 topology; supplied antibody evidence). Compare vesicular signal with the expected membrane distribution (HPA: subcellular summary; UniProt Q9NX76 subcellular annotation).
How can I reduce diffuse brown background without losing CMTM6 signal?
First inspect a no primary control for chromogen deposition and a matched tissue control for specific staining (standard chromogenic IHC practice). Quench endogenous peroxidase before DAB development, and block nonspecific antibody binding using conditions compatible with the detection system (standard IHC practice). Titrate the primary around the documented 1:100 tissue image dilution, recognizing that this caption does not establish an optimum for every specimen (A14107 tissue IHC caption). Shorten development or strengthen washes only after checking that positive cell staining remains visible (standard IHC practice). Score structured cellular signal separately from diffuse pigment, necrotic areas, and section edges (standard IHC interpretation).
How should I score CMTM6 when membrane and cytoplasmic staining differ? ⚠ ANSWER MARKED FOR VERIFICATION
Define the scored cell population and compartment before reviewing specimen groups, then keep those rules fixed (standard IHC scoring practice). Report the percentage of positive cells and staining intensity; an H-score can combine percentages at intensity levels 0–3 (standard IHC scoring practice). If cells are counted by area, report positive cells per mm² of viable tissue and the area examined (standard IHC quantification practice). Normalize cell based scores to the number of evaluable cells of the same type, rather than all nuclei when cell composition varies (standard IHC quantification practice). Record membrane and cytoplasmic scores separately because both locations are biologically plausible (UniProt Q9NX76 subcellular annotation; HPA: tissue IHC profile).
When is a strong CMTM6 stain convincing rather than artefactual?
A convincing pattern follows intact cells and plausible compartments: cell membrane or endosomal staining is expected (UniProt Q9NX76 subcellular annotation), and tissue IHC is commonly cytoplasmic (HPA: tissue IHC profile). Check the stained cell type against the specimen context; endometrial glandular cells are reported High, whereas skeletal myocytes are Not detected (HPA: tissue IHC). Treat staining confined to folds, torn edges, or necrotic regions cautiously, and examine a no primary control for endogenous enzyme signal (standard IHC practice). Recheck discordant regions at higher magnification and across adjacent sections before calling them positive (standard IHC interpretation). CMTM6 staining alone does not demonstrate functional PD-L1 stabilization, despite their reported interaction (UniProt Q9NX76 function and subunit annotation).
Boster reagents
Best CMTM6 / CKLF-like MARVEL transmembrane domain-containing protein 6 IHC Antibodies
A14107 has real IHC data from a paraffin-embedded human oophoroma section (catalog image caption); IF is listed without an IF figure, and Human and Mouse are listed as reactive species (catalog).
Real IHC data
Anti-CMTM6 Antibody
Cat # A14107
A14107 will render with an IHC image of paraffin-embedded human oophoroma at 1:100 (catalog image caption). Its listed applications include IHC and IF, and its listed reactivity is Human and Mouse (catalog); no IF image is supplied (catalog).
Which to pick: For tissue IHC, choose A14107: its own image caption documents staining of a paraffin-embedded human section at 1:100, while its IHC dilution range is 1:100–1:300 (catalog). For IF, A14107 lists IF with a dilution of 1:50, but the payload provides no IF image or ICC validation (catalog). A14107 also lists Human and Mouse reactivity (catalog); the IHC image documents human tissue only, and its fixative is unreported (catalog image caption).
Each figure is that product's own IHC / IF validation image from its datasheet.
References
- UniProt Consortium. UniProt entry Q9NX76 (CKLF6_HUMAN, CKLF-like MARVEL transmembrane domain-containing protein 6).
- Human Protein Atlas. CMTM6 tissue IHC expression (reliability: Enhanced).
- Human Protein Atlas. CMTM6 subcellular location (ICC-IF): Mainly localized to vesicles..
- Human Protein Atlas. CMTM6 antibody validation summary (2 antibodies).
- Co-expression of CMTM6 and PD-L1: a novel prognostic indicator of gastric cancer. Cancer cell international 2021 — PMC7842018.
- High membrane expression of CMTM6 in hepatocellular carcinoma is associated with tumor recurrence. Cancer science 2021 — PMC8353897.
- Molecular and immunological characteristics of patients with CMTM6 low expression colorectal cancer. Medicine 2023 — PMC10727655.
- Association of CMTM6 expression with clinicopathological characteristics and prognostic implications in renal cell carcinoma. Therapeutic advances in medical oncology 2026 — PMC13039633.
- PubMed PMID:12782130 — UniProt-cited evidence.
- PubMed PMID:14702039 — UniProt-cited evidence.
- PubMed PMID:15489334 — UniProt-cited evidence.
Immunohistochemistry protocol sheet for CMTM6 (CKLF-like MARVEL transmembrane domain-containing protein 6). Expected localisation Cytoplasmic tissue staining (HPA tissue IHC); membrane and endosomes (UniProt). Antigen retrieval: Citrate pH 6.0 HIER, 95–98 °C, 20 min (rule: cytoplasmic / membrane antigen). Validated IHC antibody: A14107 at 1:100-1:300 (the product's own IHC validation image is shown). Controls (HPA): positive Cerebellum (Purkinje cells); negative Hippocampus. IHC workflow; specimen preparation unspecified. Protocol steps: 1. Sample: Paraffin-embedded human oophoroma tissue; fixative not specified (datasheet A14107); 2. Fixation: Image fixative and duration unreported (datasheet A14107); verify before use.; 3. Sectioning: 4–5 µm sections on charged slides (standard); 4. Deparaffinisation: Xylene, graded ethanol series to water (standard); 5. Antigen retrieval: Heat-induced epitope retrieval in citrate buffer, pH 6.0 , 20 min at 95–98 °C…; 6. Peroxidase block: 3% H2O2, 10 min , room temperature (standard); 7. Blocking: 10% normal serum of the secondary host, 30 min , room temperature (standard); 8. Primary antibody: Rabbit anti-CMTM6, 1:100-1:300 (datasheet A14107); 9. Primary incubation: Overnight at 4 °C (standard). Watch for: Fixation: Keep fixation consistent across sections (standard IHC practice; not target-specific); Caveat: Antibody staining and RNA show medium consistency (HPA tissue IHC); Isoform / epitope: No isoforms listed; epitope side matters across 4 membrane spans (UniProt); Regulation: No CMTM6-specific induction reported (UniProt). Evidence: UniProt Q9NX76, HPA tissue IHC · Enhanced, HPA ICC-IF · Mainly localized to vesicles., Datasheet A14107, PMC7842018, PMC8353897. QR code links to https://www.bosterbio.com/bosterbio-gene-info-cards/CMTM6/immunohistochemistry-ihc-guide.