BIN1 p.Leu430=
c.1290G>T · VCV4956687
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,586,186)
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 0.43, phastCons 1 |
| Overall | ||
| CADD | 11.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,586,186). 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
- BIN1
- Protein
- p.Leu430=
- Coding
- c.1290G>T
- MANE Select
- NM_139343
- Type
- single nucleotide variant
- Location
- chr2:127052336 (GRCh38)
- Gene constraint
- LOEUF 0.817 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 68.61 · 7 PDB
- Residue 430
- the 'disordered' region
Similar variants
- BIN1 p.Arg145Cys Likely pathogenic ★★ same type
- BIN1 p.Arg234Cys Pathogenic/Likely pathogenic ★★ same type
- BIN1 c.165+6T>C Uncertain significance ★★ same type
- BIN1 c.-163T>C Uncertain significance ★★ same type
- BIN1 p.Ala104Ser Uncertain significance ★★ ⚠ same type
- BIN1 p.Ala289Thr Uncertain significance ★★ ⚠ same type
- BIN1 p.Ala289Val Uncertain significance ★★ ⚠ same type
- BIN1 p.Ala322Val 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/bin1-p-leu430 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown