ERVFRD-1

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

Basic information

Region (hg38): 6:11102324-11111845

Links

ENSG00000244476 ∙ NCBI:405754 ∙ OMIM:610524 ∙ HGNC:33823 ∙ Uniprot:P60508 ∙ 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 ERVFRD-1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERVFRD-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						0
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in ERVFRD-1

This is a list of pathogenic ClinVar variants found in the ERVFRD-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
6-11103848-C-A		not specified	Uncertain significance (May 01, 2022)
6-11104505-A-G		not specified	Uncertain significance (Apr 13, 2022)
6-11104526-A-G		not specified	Uncertain significance (Feb 14, 2023)
6-11104541-A-G		not specified	Uncertain significance (Oct 26, 2021)
6-11104551-C-T		not specified	Likely benign (Dec 25, 2024)
6-11104610-C-T		not specified	Uncertain significance (Aug 23, 2021)
6-11104637-G-A		not specified	Uncertain significance (Jan 10, 2023)
6-11104682-G-C		not specified	Uncertain significance (Aug 13, 2021)
6-11104691-A-G		not specified	Uncertain significance (Apr 24, 2024)
6-11104715-G-A		not specified	Uncertain significance (Jun 07, 2024)
6-11104740-G-A		not specified	Uncertain significance (Dec 15, 2023)
6-11104757-A-C		not specified	Uncertain significance (Aug 02, 2021)
6-11104788-G-A		not specified	Uncertain significance (Oct 27, 2021)
6-11104812-G-A		not specified	Uncertain significance (Jan 22, 2025)
6-11104910-C-A		not specified	Uncertain significance (Dec 04, 2024)
6-11104928-A-T		not specified	Uncertain significance (Nov 13, 2024)
6-11104937-A-G		not specified	Uncertain significance (Jun 07, 2023)
6-11104961-A-G		not specified	Uncertain significance (Nov 13, 2024)
6-11104964-T-C		not specified	Uncertain significance (Jul 14, 2021)
6-11105001-G-A		not specified	Uncertain significance (Oct 14, 2023)
6-11105076-C-A		not specified	Uncertain significance (Oct 06, 2024)
6-11105079-A-C		not specified	Uncertain significance (Apr 25, 2022)
6-11105102-G-A		not specified	Uncertain significance (Jan 08, 2024)
6-11105129-G-A		not specified	Uncertain significance (Aug 22, 2023)
6-11105258-C-T		not specified	Uncertain significance (Aug 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERVFRD-1	protein_coding	protein_coding	ENST00000472091	1	9244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0259	0.800	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	245	298	0.823	0.0000166	3467
Missense in Polyphen		48	67.084	0.71552		774
Synonymous	1.62	90	112	0.805	0.00000609	1134
Loss of Function	1.02	3	5.60	0.535	3.08e-7	61

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000915	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000619	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This endogenous retroviral envelope protein has retained its original fusogenic properties and participates in trophoblast fusion and the formation of a syncytium during placenta morphogenesis. The interaction with MFSD2A is apparently important for this process (PubMed:18988732). {ECO:0000269|PubMed:18988732}.

Intolerance Scores

• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.247
• ghis: 0.394

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Synb
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); embryo phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: syncytium formation by plasma membrane fusion;syncytium formation
• Cellular component: plasma membrane;integral component of membrane