SNAPC4 p.Pro1105=
c.3315C>T · VCV4905661
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00775%, 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 1.1 | GERP -2, phastCons 0.27 |
| Overall | ||
| CADD | 6.653 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00775%
European (non-Finnish) · 91/1,174,778 alleles
Filtering AF
0.00642%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00595%
Overall
0.00635%
101/1,591,268 alleles · very rare
exomes 95/1,439,136 · genomes 6/152,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00775% | 12,910 |
| Remaining individualsnot grpmax-eligible | 0.00647% | 15,445 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00346% | 28,932 |
| African / African-American | 0.00268% | 37,319 |
| East Asian | 0.00224% | 44,618 |
| South Asian | 0.00223% | 44,820 |
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.Pro1105=
- Coding
- c.3315C>T
- MANE Select
- NM_003086
- Type
- single nucleotide variant
- Location
- chr9:136378512 (GRCh38)
- Gene constraint
- LOEUF 0.995 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 53.61 · 18 PDB
- Residue 1105
- 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-pro1105 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown