EFNB1 p.Ser39fs
c.101_114dup · rs879255545 · VCV235545
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 5 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.3 | GERP 1.7, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- EFNB1
- Protein
- p.Ser39fs
- Coding
- c.101_114dup
- MANE Select
- NM_004429
- dbSNP
- rs879255545
- Type
- Duplication
- Location
- chrX:68829868 (GRCh38)
- Structure
- AlphaFold pLDDT 71.68 · 1 PDB
- Residue 39
- the ephrin rbd domain
Similar variants
- EFNB1 p.Ala29fs Pathogenic ★ same type
- EFNB1 p.Arg109fs Pathogenic ★ same type
- EFNB1 p.Thr135fs Pathogenic ★ same type
- EFNB1 p.Val189fs Pathogenic ★ same type
- EFNB1 p.Ala242fs Uncertain significance ★ 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-ser39fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown