HAVCR1

hepatitis A virus cellular receptor 1, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 5:157026741-157069396

Links

ENSG00000113249 ∙ NCBI:26762 ∙ OMIM:606518 ∙ HGNC:17866 ∙ Uniprot:Q96D42 ∙ 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 HAVCR1 gene.

• Inborn genetic diseases (17 variants)
• not provided (10 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HAVCR1 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				2	2	4
missense			14	4	3	21
nonsense						0
start loss						0
frameshift						0
inframe indel					2	2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	6	7

Variants in HAVCR1

This is a list of pathogenic ClinVar variants found in the HAVCR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-157029698-C-T		HAVCR1-related disorder	Benign (Sep 11, 2019)
5-157029720-G-T		HAVCR1-related disorder	Benign (Mar 12, 2019)
5-157029826-G-T		not specified	Uncertain significance (Sep 20, 2023)
5-157029851-G-T		HAVCR1-related disorder	Benign (Oct 28, 2019)
5-157032845-C-T		HAVCR1-related disorder	Benign (Oct 17, 2019)
5-157032875-T-C		not specified	Likely benign (Jun 29, 2023)
5-157037250-T-C		not specified	Uncertain significance (Nov 17, 2022)
5-157037277-G-A		not specified	Uncertain significance (Sep 25, 2023)
5-157037311-G-C		not specified	Uncertain significance (Sep 12, 2023)
5-157037313-T-G		not specified	Likely benign (Jun 10, 2022)
5-157037343-T-C		not specified	Uncertain significance (Jul 14, 2021)
5-157037349-C-T		not specified	Uncertain significance (Aug 11, 2022)
5-157052374-C-T		HAVCR1-related disorder	Likely benign (Jul 10, 2019)
5-157052412-C-T		not specified	Uncertain significance (Oct 18, 2021)
5-157052413-A-C		HAVCR1-related disorder	Benign (Oct 17, 2019)
5-157052415-T-C		HAVCR1-related disorder	Benign (Oct 17, 2019)
5-157052416-T-C		HAVCR1-related disorder	Likely benign (Feb 19, 2019)
5-157052453-G-A			Benign (Jul 23, 2018)
5-157052466-C-T		not specified	Uncertain significance (Aug 02, 2022)
5-157052468-C-T		not specified	Uncertain significance (Jul 08, 2022)
5-157052477-G-A		HAVCR1-related disorder	Benign (May 21, 2019)
5-157052479-T-C			Likely benign (Mar 01, 2023)
5-157052481-A-G		not specified	Likely benign (Jan 23, 2023)
5-157052498-A-G		HAVCR1-related disorder	Benign (Oct 17, 2019)
5-157052513-G-A		HAVCR1-related disorder	Benign (Sep 11, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HAVCR1	protein_coding	protein_coding	ENST00000339252	8	29707

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.51e-7	0.523	124657	0	137	124794	0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00775	204	204	1.00	0.0000117	2315
Missense in Polyphen		24	25.915	0.9261		308
Synonymous	-1.32	94	79.1	1.19	0.00000498	779
Loss of Function	0.833	11	14.4	0.763	7.61e-7	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000809	0.000806
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.000645	0.000645
Middle Eastern	0.0000556	0.0000556
South Asian	0.00154	0.00137
Other	0.000660	0.000660

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in T-helper cell development and the regulation of asthma and allergic diseases. Receptor for TIMD4 (By similarity). May play a role in kidney injury and repair. {ECO:0000250, ECO:0000269|PubMed:17471468}.; FUNCTION: (Microbial infection) Acts as a receptor for Ebolavirus and Marburg virus by binding exposed phosphatidyl-serine at the surface of virion membrane. {ECO:0000269|PubMed:21536871}.
• Pathway: Ebola Virus Pathway on Host;Ebola Virus Pathway on Host (Consensus)

Intolerance Scores

• loftool: 0.951
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.54

Haploinsufficiency Scores

• pHI: 0.0265
• hipred: N
• hipred_score: 0.203

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0172

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Havcr1
• Phenotype: respiratory system phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: viral entry into host cell
• Cellular component: integral component of membrane;motile cilium
• Molecular function: virus receptor activity