NBEA p.Val640Ala
c.1919T>C · VCV3369087
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.8602 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| AlphaMissense | 0.8602 | likely pathogenic |
|---|---|---|
| REVEL | 0.388 | indeterminate |
| SaProt | — | not scored · why |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 2, phastCons 1 |
| Regional constraint | o/e 0.69 | unconstrained · MANE · 86 kb · p 2.9e-12 · regional, not allelic |
| Overall | ||
| CADD | 26.2 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- NBEA
- Protein
- p.Val640Ala
- Coding
- c.1919T>C
- MANE Select
- NM_001385012
- Type
- single nucleotide variant
- Location
- chr13:35110895 (GRCh38)
- Gene constraint
- LOEUF 0.137 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Residue 640
- a UniProt-annotated variant site (in nedege)
Similar variants
- NBEA p.Val640= Likely benign ★ same residue
- NBEA p.Arg1299Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Arg145Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Arg2213Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Arg2866Ter Pathogenic ★★ same type
- NBEA p.Arg696Ter Pathogenic/Likely pathogenic ★★ same type
- NBEA p.Asp319Tyr Likely pathogenic ★★ same type
- NBEA c.4242+5G>A 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/nbea-p-val640ala (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown