EFNB1 p.Pro339=
c.1017G>A · rs773654970 · VCV2893817
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0232%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -4 |
| Overall | ||
| CADD | 1.797 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0232%
South Asian · 13/56,074 alleles
Filtering AF
0.0137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0108%
Overall
0.00555%
67/1,207,950 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0232% | 4,313 |
| European (non-Finnish) | 0.00559% | 17,884 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00455% | 21,955 |
| Remaining individualsnot grpmax-eligible | 0.00421% | 23,770 |
| African / African-American | 0.00174% | 57,471 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- EFNB1
- Protein
- p.Pro339=
- Coding
- c.1017G>A
- MANE Select
- NM_004429
- dbSNP
- rs773654970
- Type
- single nucleotide variant
- Location
- chrX:68840630 (GRCh38)
- Structure
- AlphaFold pLDDT 71.68 · 1 PDB
Similar variants
- EFNB1 c.128+1G>C Likely pathogenic ★★ same type
- EFNB1 c.499+1G>A Pathogenic/Likely pathogenic ★★ same type
- EFNB1 p.Arg66Ter Pathogenic ★★ same type
- EFNB1 p.Gln175Ter Likely pathogenic ★★ same type
- EFNB1 p.Gln85Ter Pathogenic ★★ same type
- EFNB1 p.Gly10= Pathogenic ★★ same type
- EFNB1 p.Gly151Ser Pathogenic ★★ same type
- EFNB1 p.Met158Val Pathogenic/Likely pathogenic ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/efnb1-p-pro339 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown