CMTM5

protein-coding

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

Gene summary

This gene encodes a member of the chemokine-like factor superfamily. This family of genes encodes multi-pass membrane proteins that are similar to both the chemokine and the transmembrane 4 superfamilies of signaling molecules. The encoded protein may exhibit tumor suppressor activity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

Previous symbols:

CKLFSF5

MANE transcript

NM_001288746.2

Inheritance

—

ClinVar variants

U:43B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr14:23,376,773-23,379,772

External References & Databases

Ensembl (ENSG00000166091)

Transcript & Mutation Effects

hg38 • Region Span ~3.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CMTM5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 43

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001288746.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		2 clinvar	3
missense			42 clinvar	3 clinvar		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	3	2	48

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001288746.2	RefSeq	NP_001275675.1	6	MANE Select
ENST00000339180.9	Ensembl	ENSP00000344819.4	6	MANE Select
NM_001037288.2	RefSeq	NP_001032365.1	4	Standard
NM_001288744.2	RefSeq	NP_001275673.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

chemotaxis
regulation of signaling receptor activity
negative regulation of myoblast differentiation

Molecular Function

cytokine activity
protein binding

Cellular Component

extracellular space
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359320
Coding exons: 5
Length: 2965
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125740
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0404	98	96.9	1.01	0.00000581	1007
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000044	0.000044	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0859

Intolerance Scores

LoFtool: 0.789
RVIS EVS: 0.15
RVIS percentile EVS: 64.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0277

Gene Damage Prediction

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