CMTM4

CKLF like MARVEL transmembrane domain containing 4, the group of CKLF like MARVEL transmembrane domain containing

Basic information

Region (hg38): 16:66614750-66696743

Previous symbols: [ "CKLFSF4" ]

Links

ENSG00000183723 ∙ NCBI:146223 ∙ OMIM:607887 ∙ HGNC:19175 ∙ Uniprot:Q8IZR5 ∙ 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 CMTM4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMTM4 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in CMTM4

This is a list of pathogenic ClinVar variants found in the CMTM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-66617294-G-T		not specified	Uncertain significance (Oct 13, 2021)
16-66622087-G-A		not specified	Uncertain significance (Aug 09, 2021)
16-66622114-G-A		not specified	Uncertain significance (Oct 12, 2024)
16-66622131-T-C		not specified	Uncertain significance (Dec 20, 2023)
16-66622139-C-G		not specified	Uncertain significance (Jul 08, 2022)
16-66622146-C-T		not specified	Uncertain significance (Nov 29, 2023)
16-66622179-A-T		not specified	Uncertain significance (Mar 31, 2024)
16-66622206-G-A		not specified	Uncertain significance (Sep 14, 2022)
16-66623432-T-C		not specified	Uncertain significance (May 27, 2022)
16-66623451-C-A		not specified	Uncertain significance (Nov 22, 2024)
16-66636438-G-T		not specified	Uncertain significance (Jul 22, 2024)
16-66636470-C-T		not specified	Uncertain significance (Aug 16, 2022)
16-66636556-C-G		not specified	Uncertain significance (Aug 11, 2022)
16-66696344-T-C		not specified	Uncertain significance (Aug 21, 2023)
16-66696362-C-A		not specified	Uncertain significance (Nov 17, 2023)
16-66696404-G-A		not specified	Uncertain significance (May 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMTM4	protein_coding	protein_coding	ENST00000330687	5	81958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.231	0.739	125739	0	7	125746	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	80	115	0.699	0.00000667	1513
Missense in Polyphen		24	42.214	0.56853		592
Synonymous	0.770	40	46.7	0.857	0.00000290	472
Loss of Function	1.81	2	7.26	0.276	3.93e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000286	0.000153
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000355	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a backup for CMTM6 to regulate plasma membrane expression of PD-L1/CD274, an immune inhibitory ligand critical for immune tolerance to self and antitumor immunity. May protect PD-L1/CD274 from being polyubiquitinated and targeted for degradation. {ECO:0000269|PubMed:28813410}.

Recessive Scores

• pRec: 0.0898

Intolerance Scores

• loftool: 0.669
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.207
• hipred: N
• hipred_score: 0.280
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cmtm4

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding