CMTM5

CKLF like MARVEL transmembrane domain containing 5, the group of CKLF like MARVEL transmembrane domain containing

Basic information

Region (hg38): 14:23376773-23379772

Previous symbols: [ "CKLFSF5" ]

Links

ENSG00000166091 ∙ NCBI:116173 ∙ OMIM:607888 ∙ HGNC:19176 ∙ Uniprot:Q96DZ9 ∙ 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 CMTM5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CMTM5 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					1	1
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	19	0	1

Variants in CMTM5

This is a list of pathogenic ClinVar variants found in the CMTM5 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-23377265-G-A		not specified	Uncertain significance (May 26, 2024)
14-23377274-G-A		not specified	Uncertain significance (Mar 20, 2023)
14-23377286-C-T		not specified	Uncertain significance (Nov 25, 2024)
14-23377321-G-A		not specified	Uncertain significance (Mar 03, 2022)
14-23377372-G-A		not specified	Uncertain significance (Jan 10, 2023)
14-23378349-G-T		not specified	Uncertain significance (Oct 25, 2024)
14-23378351-C-T			Benign (May 21, 2018)
14-23378356-C-A		not specified	Uncertain significance (Dec 12, 2022)
14-23378364-A-C		not specified	Uncertain significance (Sep 14, 2023)
14-23378377-T-C		not specified	Uncertain significance (Oct 13, 2023)
14-23378380-C-T		not specified	Uncertain significance (Sep 30, 2024)
14-23378410-C-T		not specified	Uncertain significance (Feb 10, 2023)
14-23378443-T-A		not specified	Uncertain significance (Mar 01, 2024)
14-23378444-C-G			Benign (May 21, 2018)
14-23378460-C-G		not specified	Uncertain significance (Dec 09, 2024)
14-23378472-C-T		not specified	Uncertain significance (Sep 09, 2021)
14-23378482-G-A		not specified	Uncertain significance (Dec 30, 2023)
14-23379035-T-A		not specified	Uncertain significance (Dec 27, 2023)
14-23379040-C-T		not specified	Uncertain significance (Mar 04, 2024)
14-23379046-G-A		not specified	Uncertain significance (Oct 13, 2023)
14-23379049-A-T		not specified	Uncertain significance (Aug 20, 2024)
14-23379058-A-G		not specified	Uncertain significance (Dec 13, 2023)
14-23379061-A-G		not specified	Uncertain significance (Jan 26, 2022)
14-23379097-C-T		not specified	Uncertain significance (Dec 16, 2022)
14-23379098-G-A		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CMTM5	protein_coding	protein_coding	ENST00000359320	5	2965

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0658	0.877	125726	0	14	125740	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0404	98	96.9	1.01	0.00000581	1007
Missense in Polyphen		34	33.857	1.0042		379
Synonymous	0.755	33	39.0	0.846	0.00000235	323
Loss of Function	1.60	3	7.85	0.382	4.64e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000362	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0859

Intolerance Scores

• loftool: 0.789
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.144
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0277

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cmtm5
• Phenotype: skeleton phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

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