GAP43 p.Asp16=
c.48C>T · rs147441474 · VCV747086
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0651%, afr)
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 0.59 | GERP -3.2, phastCons 0.99 |
| Overall | ||
| CADD | 9.532 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0651%
African / African-American · 48/73,750 alleles
Filtering AF
0.0503%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0452%
Overall
0.00613%
98/1,598,880 alleles · ultra-rare
exomes 66/1,446,850 · genomes 32/152,030 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0651% | 1,536 |
| Admixed American | 0.0175% | 5,704 |
| Remaining individualsnot grpmax-eligible | 0.0162% | 6,172 |
| East Asian | 0.0134% | 7,453 |
| European (non-Finnish) | 0.00196% | 51,045 |
| South Asian | 0.00114% | 87,982 |
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.Asp16=
- Coding
- c.48C>T
- MANE Select
- NM_002045
- dbSNP
- rs147441474
- Type
- single nucleotide variant
- Location
- chr3:115676030 (GRCh38)
- Gene constraint
- LOEUF 0.358 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 56.00
- Residue 16
- 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-asp16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown