EFNB1 p.Arg199=
c.597G>A · rs200409169 · VCV2660794
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 9.11e-05%)
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 0.76 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 3.751 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.11e-05%
Overall
9.11e-05%
1/1,098,164 alleles · very rare
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.Arg199=
- Coding
- c.597G>A
- MANE Select
- NM_004429
- dbSNP
- rs200409169
- Type
- single nucleotide variant
- Location
- chrX:68840057 (GRCh38)
- Structure
- AlphaFold pLDDT 71.68 · 1 PDB
- Residue 199
- the 'disordered' region
Similar variants
- EFNB1 p.Arg199Trp Uncertain significance ★★ ⚠ same residue
- EFNB1 p.Arg199Gln Uncertain significance ★ ⚠ same residue
- 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
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-arg199 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown