SNAPC4 p.Pro1340=
c.4020G>A · VCV4533957
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0467%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -1.5 |
| Overall | ||
| CADD | 0.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0467%
African / African-American · 35/75,026 alleles
Filtering AF
0.0345%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0302%
Overall
0.00298%
48/1,611,646 alleles · ultra-rare
exomes 28/1,459,374 · genomes 20/152,272 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0467% | 2,144 |
| East Asian | 0.00892% | 11,216 |
| Admixed American | 0.00833% | 11,998 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,434 |
| European (non-Finnish) | 0.000254% | 393,239 |
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
- SNAPC4
- Protein
- p.Pro1340=
- Coding
- c.4020G>A
- MANE Select
- NM_003086
- Type
- single nucleotide variant
- Location
- chr9:136377807 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.61 · 18 PDB
- Residue 1340
- the 'snapc2-binding' region; a UniProt-annotated variant site (in nedrso; likely pathogenic)
Similar variants
- SNAPC4 p.Ala1193Gly Uncertain significance ★★ ⚠ same type
- SNAPC4 p.Ala437Thr Uncertain significance ★★ ⚠ same type
- SNAPC4 p.Arg640Lys Uncertain significance ★★ ⚠ same type
- SNAPC4 p.Asp436Asn Uncertain significance ★★ ⚠ same type
- SNAPC4 p.Glu546Asp Uncertain significance ★★ ⚠ same type
- SNAPC4 p.Leu831Phe Uncertain significance ★★ ⚠ same type
- SNAPC4 p.Gly525Ser Likely benign ★★ same type
- SNAPC4 c.1500+1G>A Likely pathogenic ★ 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/snapc4-p-pro1340 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown