GAP43 p.Ala88=
c.264C>T · VCV4028231
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00833%, amr)
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 -5.2 |
| Overall | ||
| CADD | 0.507 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/59,990 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00124%
20/1,613,958 alleles · very rare
exomes 16/1,461,882 · genomes 4/152,076 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00833% | 11,998 |
| South Asian | 0.00659% | 15,179 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| African / African-American | 0.00267% | 37,436 |
| European (non-Finnish) | 0.000424% | 236,007 |
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
- GAP43
- Protein
- p.Ala88=
- Coding
- c.264C>T
- MANE Select
- NM_002045
- Type
- single nucleotide variant
- Location
- chr3:115676246 (GRCh38)
- Gene constraint
- LOEUF 0.358 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.00
- Residue 88
- the 'disordered' region
Similar variants
- GAP43 c.31-12223C>T Benign ★★ same type
- GAP43 c.31-12167G>A Uncertain significance ★ same type
- GAP43 c.31-12204C>T Uncertain significance ★ same type
- GAP43 p.Ala124Gly Uncertain significance ★ ⚠ same type
- GAP43 p.Ala135Ser Uncertain significance ★ ⚠ same type
- GAP43 p.Ala135Thr Uncertain significance ★ ⚠ same type
- GAP43 p.Ala146Ser Uncertain significance ★ ⚠ same type
- GAP43 p.Ala178Ser 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/gap43-p-ala88 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown