CMTM7

CKLF like MARVEL transmembrane domain containing 7, the group of CKLF like MARVEL transmembrane domain containing

Basic information

Region (hg38): 3:32391697-32483067

Previous symbols: [ "CKLFSF7" ]

Links

ENSG00000153551 ∙ NCBI:112616 ∙ OMIM:607890 ∙ HGNC:19178 ∙ Uniprot:Q96FZ5 ∙ 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 CMTM7 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMTM7 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in CMTM7

This is a list of pathogenic ClinVar variants found in the CMTM7 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-32391935-C-T		not specified	Uncertain significance (Mar 29, 2022)
3-32391937-A-C		not specified	Uncertain significance (Dec 19, 2023)
3-32391961-G-C		not specified	Uncertain significance (Jul 26, 2022)
3-32391996-C-A		not specified	Uncertain significance (Jan 30, 2024)
3-32441897-G-A		not specified	Uncertain significance (Aug 20, 2023)
3-32441922-C-A		not specified	Uncertain significance (Nov 21, 2022)
3-32441984-G-A		not specified	Uncertain significance (Mar 25, 2022)
3-32441984-G-C		not specified	Uncertain significance (May 05, 2023)
3-32449469-T-G		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMTM7	protein_coding	protein_coding	ENST00000334983	5	91397

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0382	0.847	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.950	55	78.7	0.699	0.00000485	1121
Missense in Polyphen		16	27.186	0.58853		359
Synonymous	-0.0256	33	32.8	1.01	0.00000223	369
Loss of Function	1.27	3	6.49	0.462	2.75e-7	91

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.346
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.102
• hipred: N
• hipred_score: 0.332
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.113

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cmtm7
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype

Gene ontology

• Biological process: B-1a B cell differentiation;chemotaxis;regulation of signaling receptor activity
• Cellular component: extracellular space;membrane;integral component of membrane
• Molecular function: cytokine activity