CD160

protein-coding

CD160 molecule, the group of Immunoglobulin like domain containing|CD molecules

Gene summary

CD160 is an 27 kDa glycoprotein which was initially identified with the monoclonal antibody BY55. Its expression is tightly associated with peripheral blood NK cells and CD8 T lymphocytes with cytolytic effector activity. The cDNA sequence of CD160 predicts a cysteine-rich, glycosylphosphatidylinositol-anchored protein of 181 amino acids with a single Ig-like domain weakly homologous to KIR2DL4 molecule. CD160 is expressed at the cell surface as a tightly disulfide-linked multimer. RNA blot analysis revealed CD160 mRNAs of 1.5 and 1.6 kb whose expression was highly restricted to circulating NK and T cells, spleen and small intestine. Within NK cells CD160 is expressed by CD56dimCD16+ cells whereas among circulating T cells its expression is mainly restricted to TCRgd bearing cells and to TCRab+CD8brightCD95+CD56+CD28-CD27-cells. In tissues, CD160 is expressed on all intestinal intraepithelial lymphocytes. CD160 shows a broad specificity for binding to both classical and nonclassical MHC class I molecules. [provided by RefSeq, Jul 2008]

MANE transcript

NM_007053.4

Inheritance

—

ClinVar variants

U:23B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr1:145,719,471-145,739,288

External References & Databases

Ensembl (ENSG00000117281)

Transcript & Mutation Effects

hg38 • Region Span ~19.8 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 CD160 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 17

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007053.4. 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						0
missense			18 clinvar	1 clinvar	1 clinvar	20
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	23	1	1	25

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007053.4	RefSeq	NP_008984.1	4	MANE Select
ENST00000369288.7	Ensembl	ENSP00000358294.1	4	MANE Select
ENST00000235933.10	Ensembl	ENSP00000235933.6	4	Standard
ENST00000235933.11	Ensembl	ENSP00000235933.6	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Immune System
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Adaptive Immune System

Biological Process

cellular defense response
cell surface receptor signaling pathway
cell population proliferation
negative regulation of angiogenesis
regulation of immune response

Molecular Function

signaling receptor binding
protein binding
MHC class I receptor activity
signaling receptor activity

Cellular Component

plasma membrane
anchored component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000235933
Coding exons: 4
Length: 19817
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125739
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.424	84	95.7	0.878	0.00000470	1172
Missense (PolyPhen)		12	20.629	0.5817		283
Synonymous	0.255	36	38.0	0.947	0.00000200	354
Loss of Function	0.499	7	8.58	0.816	4.47e-7	103

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Receptor showing broad specificity for both classical and non-classical MHC class I molecules. {ECO:0000269|PubMed:9973372}.;

Recessive Scores

pRec: 0.0895

Intolerance Scores

LoFtool: 0.773
RVIS EVS: -0.07
RVIS percentile EVS: 48.12

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.450

Gene Damage Prediction

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