CD160

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

Basic information

Region (hg38): 1:145719471-145739288

Links

ENSG00000117281

∙ NCBI:11126 ∙ OMIM:604463 ∙ HGNC:17013 ∙ Uniprot:O95971 ∙ 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 CD160 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD160 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			5 clinvar		1 clinvar	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	1

Variants in CD160

This is a list of pathogenic ClinVar variants found in the CD160 region.

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

Position	Phenotype	Significance	ClinVar
1-145728382-G-A	not specified	Uncertain significance (Jan 26, 2022)	3140295
1-145730786-G-A	not specified	Likely benign (May 21, 2024)	3264719
1-145730920-G-A		Benign (Jul 31, 2018)	718727
1-145730987-A-G	not specified	Uncertain significance (Jan 04, 2022)	2412299
1-145731020-A-G	not specified	Uncertain significance (Jan 17, 2023)	3140294
1-145731034-C-T	not specified	Uncertain significance (May 24, 2023)	2512734
1-145736048-T-A	not specified	Uncertain significance (Jun 22, 2023)	2593395

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD160	protein_coding	protein_coding	ENST00000235933	4	19817

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000684	0.510	125729	0	10	125739	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.424	84	95.7	0.878	0.00000470	1172
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.000133	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Receptor showing broad specificity for both classical and non-classical MHC class I molecules. {ECO:0000269|PubMed:9973372}.;
Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

pRec: 0.0895

Intolerance Scores

loftool: 0.773
rvis_EVS: -0.07
rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

pHI: 0.0871
hipred: N
hipred_score: 0.123
ghis: 0.425

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.450

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cd160
Phenotype: immune system phenotype; neoplasm;

Gene ontology

Biological process: cellular defense response;cell surface receptor signaling pathway;cell population proliferation;negative regulation of angiogenesis;regulation of immune response;defense response to Gram-negative bacterium;positive regulation of endothelial cell apoptotic process
Cellular component: plasma membrane;anchored component of plasma membrane
Molecular function: signaling receptor binding;protein binding;MHC class I receptor activity;signaling receptor activity