SPART p.Pro162=
c.486A>G · rs368226366 · VCV1145676
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0507%, 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 -12 | GERP -2.2 |
| Overall | ||
| CADD | 0.095 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0507%
African / African-American · 38/75,020 alleles
Filtering AF
0.0379%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0334%
Overall
0.00514%
83/1,614,076 alleles · ultra-rare
exomes 55/1,461,802 · genomes 28/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0507% | 1,974 |
| Admixed American | 0.01% | 10,002 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,501 |
| European (non-Finnish) | 0.00288% | 34,706 |
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
- SPART
- Protein
- p.Pro162=
- Coding
- c.486A>G
- MANE Select
- NM_015087
- dbSNP
- rs368226366
- Type
- single nucleotide variant
- Location
- chr13:36335345 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.03 · 2 PDB
Similar variants
- SPART p.Arg457Ter Pathogenic ★★ same type
- SPART p.Gln229Ter Pathogenic/Likely pathogenic ★★ same type
- SPART p.Ala152Thr Uncertain significance ★★ ⚠ same type
- SPART p.Ala157Thr Uncertain significance ★★ ⚠ same type
- SPART p.Ala236Ser Uncertain significance ★★ ⚠ same type
- SPART p.Ala23Asp Uncertain significance ★★ ⚠ same type
- SPART p.Ala472Pro Uncertain significance ★★ same type
- SPART p.Arg249Gln 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/spart-p-pro162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown