EFNB2 p.Ser260=
c.780G>A · VCV3352657
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.56%, nfe)
Conditions
1
EFNB2-related disorder
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 -4.8 | GERP -5.8 |
| Overall | ||
| CADD | 5.864 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.56%
European (non-Finnish) · 30,179/1,180,026 alleles
Filtering AF
2.53%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.52%
Overall
2.16%
34,918/1,614,152 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 2.56% | 39 |
| Ashkenazi Jewishnot grpmax-eligible | 2.25% | 44 |
| Remaining individualsnot grpmax-eligible | 2.04% | 49 |
| Finnishnot grpmax-eligible | 1.97% | 51 |
| Middle Eastern | 1.29% | 78 |
| Admixed American | 1.09% | 91 |
| South Asian | 0.545% | 184 |
| Amishnot grpmax-eligible | 0.439% | 228 |
| African / African-American | 0.402% | 249 |
| East Asian | 0.00446% | 22,434 |
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
- EFNB2
- Protein
- p.Ser260=
- Coding
- c.780G>A
- MANE Select
- NM_004093
- Type
- single nucleotide variant
- Location
- chr13:106493262 (GRCh38)
- Gene constraint
- LOEUF 0.261 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 71.60 · 10 PDB
- Residue 260
- a modified residue (phosphoserine)
Disease context
EFNB2-related disorder
Similar variants
- EFNB2 p.Cys301Tyr Uncertain significance ★ ⚠ same condition
- EFNB2 c.614-8G>A Likely benign same condition
- EFNB2 p.Leu221= Likely benign same condition
- EFNB2 p.Pro261= Likely benign same condition
- EFNB2 p.Ser38= Likely benign same condition
- EFNB2 p.Tyr73Ter Likely pathogenic ★ same type
- EFNB2 p.Ala157Thr Uncertain significance ★ ⚠ same type
- EFNB2 p.Ala296Ser 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/efnb2-p-ser260 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown