CMTM3

CKLF like MARVEL transmembrane domain containing 3, the group of CKLF like MARVEL transmembrane domain containing

Basic information

Region (hg38): 16:66603874-66613892

Previous symbols: [ "CKLFSF3" ]

Links

ENSG00000140931 ∙ NCBI:123920 ∙ OMIM:607886 ∙ HGNC:19174 ∙ Uniprot:Q96MX0 ∙ 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 CMTM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMTM3 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 CMTM3

This is a list of pathogenic ClinVar variants found in the CMTM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-66604845-C-A		not specified	Uncertain significance (Jun 24, 2022)
16-66604887-C-T		not specified	Uncertain significance (Jan 23, 2024)
16-66604890-G-A		not specified	Uncertain significance (Aug 21, 2023)
16-66604949-G-C		not specified	Uncertain significance (Mar 28, 2024)
16-66608343-C-T		not specified	Uncertain significance (May 27, 2022)
16-66609483-A-G		not specified	Uncertain significance (Jun 18, 2021)
16-66609502-A-G		not specified	Uncertain significance (Jul 25, 2023)
16-66609905-T-C		not specified	Uncertain significance (Sep 01, 2021)
16-66609982-A-C		not specified	Uncertain significance (Mar 20, 2024)
16-66612624-C-T		not specified	Uncertain significance (Apr 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMTM3	protein_coding	protein_coding	ENST00000424011	5	10019

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000150	0.442	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.525	76	90.0	0.844	0.00000510	1155
Missense in Polyphen		27	34.613	0.78005		407
Synonymous	0.518	38	42.3	0.899	0.00000287	377
Loss of Function	0.230	6	6.64	0.904	2.81e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.373
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.398
• ghis: 0.658

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cmtm3

Gene ontology

• Biological process: blastocyst hatching;chemotaxis;regulation of signaling receptor activity;positive regulation of B cell receptor signaling pathway
• Cellular component: extracellular space;cytoplasm;integral component of membrane;nuclear membrane
• Molecular function: cytokine activity;protein binding