SPART p.Ser243=
c.729G>A · rs752668390 · VCV2048313
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
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 -9.4 | GERP -3.5 |
| Overall | ||
| CADD | 1.998 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,000 alleles
Filtering AF
0.00103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00083%
Overall
0.00149%
24/1,613,984 alleles · very rare
exomes 21/1,461,846 · genomes 3/152,138 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,000 |
| East Asian | 0.00223% | 44,892 |
| European (non-Finnish) | 0.00161% | 62,106 |
| African / African-American | 0.00134% | 74,906 |
| South Asian | 0.0011% | 91,078 |
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.Ser243=
- Coding
- c.729G>A
- MANE Select
- NM_015087
- dbSNP
- rs752668390
- Type
- single nucleotide variant
- Location
- chr13:36335102 (GRCh38)
- Gene constraint
- LOEUF 0.759 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.03 · 2 PDB
- Residue 243
- the 'ubiquitin-binding region (ubr) domain' region
Similar variants
- SPART p.Ser243Leu Uncertain significance ★★ ⚠ same residue
- 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
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-ser243 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown