CMTM2

CKLF like MARVEL transmembrane domain containing 2, the group of CKLF like MARVEL transmembrane domain containing

Basic information

Region (hg38): 16:66579447-66588275

Previous symbols: [ "CKLFSF2" ]

Links

ENSG00000140932 ∙ NCBI:146225 ∙ OMIM:607885 ∙ HGNC:19173 ∙ Uniprot:Q8TAZ6 ∙ 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 CMTM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMTM2 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			12	2		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	0

Variants in CMTM2

This is a list of pathogenic ClinVar variants found in the CMTM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-66579657-C-A		not specified	Uncertain significance (Dec 19, 2022)
16-66579806-G-A		not specified	Uncertain significance (Jan 26, 2022)
16-66579815-C-T		not specified	Uncertain significance (Sep 29, 2023)
16-66579843-A-G		not specified	Uncertain significance (Jun 03, 2024)
16-66579864-G-T		not specified	Uncertain significance (Nov 27, 2023)
16-66580150-A-G		not specified	Uncertain significance (Nov 21, 2022)
16-66580160-A-G		not specified	Likely benign (Mar 06, 2023)
16-66587042-G-A		not specified	Uncertain significance (Nov 10, 2022)
16-66587045-G-A		not specified	Uncertain significance (Jun 02, 2023)
16-66587063-C-T		not specified	Uncertain significance (Nov 07, 2022)
16-66587067-G-A		not specified	Likely benign (May 23, 2023)
16-66587988-A-G		not specified	Uncertain significance (Jun 02, 2023)
16-66588024-G-A		not specified	Uncertain significance (Jul 14, 2023)
16-66588036-G-A		not specified	Uncertain significance (May 18, 2023)
16-66588063-C-T		not specified	Uncertain significance (May 11, 2022)
16-66588094-C-T		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMTM2	protein_coding	protein_coding	ENST00000268595	4	8828

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000294	0.348	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.355	138	150	0.918	0.00000888	1621
Missense in Polyphen		37	41.733	0.88659		460
Synonymous	1.19	47	58.6	0.802	0.00000414	491
Loss of Function	0.116	7	7.34	0.954	3.13e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000813	0.000813
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Coregulation of Androgen receptor activity (Consensus)

Recessive Scores

• pRec: 0.0705

Intolerance Scores

• loftool: 0.808
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.73

Haploinsufficiency Scores

• pHI: 0.0500
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.492

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cmtm2b

Gene ontology

• Biological process: chemotaxis;regulation of signaling receptor activity
• Cellular component: extracellular space;integral component of membrane
• Molecular function: cytokine activity