SNAPC4 p.Pro1052=
c.3156A>C · VCV3778011
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00045%, nfe)
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 -0.38 | GERP -2.1 |
| Overall | ||
| CADD | 1.544 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00045%
European (non-Finnish) · 5/1,110,138 alleles
Filtering AF
0.000132%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.6e-05%
Overall
0.00034%
5/1,471,652 alleles · very rare
exomes 5/1,332,556 · genomes 0/139,096 · joint denominator
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.Pro1052=
- Coding
- c.3156A>C
- MANE Select
- NM_003086
- Type
- single nucleotide variant
- Location
- chr9:136378671 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.61 · 18 PDB
- Residue 1052
- a UniProt-annotated variant site (in nedrso; likely pathogenic)
Similar variants
- SNAPC4 p.Pro1052Leu Uncertain significance ★ ⚠ same residue
- 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
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-pro1052 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown