CMTM6

CKLF like MARVEL transmembrane domain containing 6, the group of CKLF like MARVEL transmembrane domain containing

Basic information

Region (hg38): 3:32481312-32502852

Previous symbols: [ "CKLFSF6" ]

Links

ENSG00000091317 ∙ NCBI:54918 ∙ OMIM:607889 ∙ HGNC:19177 ∙ Uniprot:Q9NX76 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CMTM6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMTM6 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in CMTM6

This is a list of pathogenic ClinVar variants found in the CMTM6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-32484064-G-A		not specified	Uncertain significance (Apr 18, 2023)
3-32484084-A-G		not specified	Uncertain significance (Feb 07, 2023)
3-32491883-G-C		not specified	Uncertain significance (Oct 25, 2022)
3-32502651-C-A		not specified	Uncertain significance (Jun 06, 2023)
3-32502654-A-G		not specified	Uncertain significance (Mar 18, 2024)
3-32502681-C-T		not specified	Uncertain significance (Mar 16, 2022)
3-32502699-C-G		not specified	Uncertain significance (Jun 22, 2021)
3-32502714-G-A		not specified	Uncertain significance (May 23, 2023)
3-32502729-A-C		not specified	Uncertain significance (Jul 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMTM6	protein_coding	protein_coding	ENST00000205636	4	22097

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.433	0.539	125702	0	4	125706	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.505	74	87.3	0.848	0.00000389	1156
Missense in Polyphen		15	32.014	0.46855		465
Synonymous	-0.294	35	32.9	1.07	0.00000142	369
Loss of Function	1.75	1	5.38	0.186	2.23e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000335	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Master regulator of recycling and plasma membrane expression of PD-L1/CD274, an immune inhibitory ligand critical for immune tolerance to self and antitumor immunity. Associates with both constitutive and IFNG-induced PD-L1/CD274 at recycling endosomes, where it protects PD-L1/CD274 from being targeted for lysosomal degradation, likely by preventing its STUB1-mediated ubiquitination. May stabilize PD-L1/CD274 expression on antigen presenting cells and potentiates inhibitory signaling by PDCD1/CD279, its receptor on T-cells, ultimately triggering T-cell anergy. {ECO:0000269|PubMed:28813410, ECO:0000269|PubMed:28813417}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0943

Intolerance Scores

• loftool: 0.347
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.76

Haploinsufficiency Scores

• pHI: 0.153
• hipred: N
• hipred_score: 0.226
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cmtm6

Gene ontology

• Biological process: protein transport;regulation of protein stability;endocytic recycling;neutrophil degranulation
• Cellular component: plasma membrane;membrane;integral component of membrane;early endosome membrane;azurophil granule membrane;specific granule membrane;recycling endosome membrane
• Molecular function: protein binding