ERBIN p.Leu259=
c.777A>G · VCV3694641
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
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 -5.4 | GERP -12 |
| Overall | ||
| CADD | 1.288 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,032 alleles
Filtering AF
0.00959%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00768%
Overall
0.00106%
17/1,603,436 alleles · ultra-rare
exomes 14/1,451,250 · genomes 3/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,032 |
| South Asian | 0.0159% | 6,295 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,118 |
| European (non-Finnish) | 8.49e-05% | 1,177,292 |
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
- ERBIN
- Protein
- p.Leu259=
- Coding
- c.777A>G
- MANE Select
- NM_001253697
- Type
- single nucleotide variant
- Location
- chr5:66024410 (GRCh38)
- Gene constraint
- LOEUF 0.526 · pLI 0.72 (gnomAD)
- Structure
- AlphaFold pLDDT 56.01 · 11 PDB
Similar variants
- ERBIN p.Ala942Val Uncertain significance ★★ ⚠ same type
- ERBIN p.Arg1096Gln Uncertain significance ★★ ⚠ same type
- ERBIN p.Arg1166Gln Uncertain significance ★★ ⚠ same type
- ERBIN p.Asn1035Ser Uncertain significance ★★ ⚠ same type
- ERBIN p.Asn650Ser Uncertain significance ★★ ⚠ same type
- ERBIN p.Asp530Tyr Uncertain significance ★★ ⚠ same type
- ERBIN p.Cys658Ser Uncertain significance ★★ ⚠ same type
- ERBIN p.His521Arg 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/erbin-p-leu259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown