ERV3-1

endogenous retrovirus group 3 member 1, envelope, the group of Envelope ERV derived genes

Basic information

Region (hg38): 7:64990355-65006743

Previous symbols: [ "ERV3" ]

Links

ENSG00000213462 ∙ NCBI:2086 ∙ OMIM:131170 ∙ HGNC:3454 ∙ Uniprot:Q14264 ∙ 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 ERV3-1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERV3-1 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			1		1	2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	2

Variants in ERV3-1

This is a list of pathogenic ClinVar variants found in the ERV3-1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-64991268-T-C		not specified	Uncertain significance (May 01, 2022)
7-64991329-T-C			Benign (Aug 02, 2017)
7-64992198-C-T			Benign (Aug 02, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERV3-1	protein_coding	protein_coding	ENST00000394323	1	15935

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.733	364	327	1.11	0.0000165	3890
Missense in Polyphen		61	71.879	0.84865		970
Synonymous	-0.326	129	124	1.04	0.00000674	1183
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Retroviral envelope proteins mediate receptor recognition and membrane fusion during early infection. Endogenous envelope proteins may have kept, lost or modified their original function during evolution. This endogenous envelope protein has lost its fusogenic properties. It can inhibit cell growth through decrease expression of cyclin B1 and increased expression of p21 in vitro. {ECO:0000269|PubMed:10692254, ECO:0000269|PubMed:14557543, ECO:0000269|PubMed:7645262}.; FUNCTION: TM anchors the envelope heterodimer to the viral membrane through one transmembrane domain. The other hydrophobic domain, called fusion peptide, mediates fusion of the viral membrane with the target cell membrane (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: 1.94
• rvis_percentile_EVS: 97.52

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.146
• ghis: 0.409

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: biological_process
• Molecular function: molecular_function