CMTM1

CKLF like MARVEL transmembrane domain containing 1, the group of CKLF like MARVEL transmembrane domain containing

Basic information

Region (hg38): 16:66566393-66579137

Previous symbols: [ "CKLFSF1" ]

Links

ENSG00000089505 ∙ NCBI:113540 ∙ OMIM:607884 ∙ HGNC:19172 ∙ Uniprot:Q8IZ96 ∙ 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 CMTM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMTM1 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in CMTM1

This is a list of pathogenic ClinVar variants found in the CMTM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-66566526-C-T		not specified	Uncertain significance (Jun 05, 2023)
16-66566599-G-A		not specified	Uncertain significance (Oct 20, 2024)
16-66566607-A-G		not specified	Uncertain significance (Jan 08, 2024)
16-66566676-G-A		not specified	Uncertain significance (Jun 24, 2022)
16-66566688-C-T		not specified	Uncertain significance (Oct 12, 2024)
16-66566692-G-C		not specified	Likely benign (Dec 05, 2022)
16-66566709-G-A		not specified	Likely benign (Aug 02, 2021)
16-66566742-C-G		not specified	Uncertain significance (Oct 04, 2024)
16-66566769-C-G		not specified	Uncertain significance (Apr 27, 2023)
16-66566772-C-T		not specified	Uncertain significance (Mar 15, 2024)
16-66566794-C-T		not specified	Uncertain significance (May 13, 2024)
16-66566796-A-G		not specified	Uncertain significance (Mar 01, 2023)
16-66566838-G-A		not specified	Uncertain significance (May 24, 2024)
16-66566888-G-T		not specified	Uncertain significance (Mar 29, 2023)
16-66566911-T-C		not specified	Uncertain significance (Sep 13, 2023)
16-66570056-C-G		not specified	Uncertain significance (Nov 01, 2022)
16-66570064-C-G		not specified	Uncertain significance (Aug 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMTM1	protein_coding	protein_coding	ENST00000379500	4	12747

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00224	0.775	124483	0	6	124489	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.425	168	184	0.912	0.0000114	1822
Missense in Polyphen		47	55.509	0.84671		498
Synonymous	0.446	78	83.2	0.938	0.00000599	615
Loss of Function	0.973	5	7.96	0.628	4.18e-7	106

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.000119	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00000887	0.00000884
Middle Eastern	0.000119	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0583

Intolerance Scores

• loftool: 0.975
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.0266
• hipred: N
• hipred_score: 0.182
• ghis: 0.390

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.176

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cmtm1

Gene ontology

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