SACS p.Pro628=
c.1884C>T · rs144468379 · VCV699248
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0733%, afr)
Conditions
2
Spastic paraplegia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.103 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.3 | GERP -3.9 |
| Overall | ||
| CADD | 0.078 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0733%
African / African-American · 55/75,056 alleles
Filtering AF
0.0578%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0522%
Overall
0.00564%
91/1,613,554 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0733% | 1,365 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,806 |
| Admixed American | 0.015% | 6,667 |
| East Asian | 0.00446% | 22,433 |
| South Asian | 0.0022% | 45,528 |
| European (non-Finnish) | 0.000848% | 117,958 |
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
- SACS
- Protein
- p.Pro628=
- Coding
- c.1884C>T
- MANE Select
- NM_014363
- dbSNP
- rs144468379
- Type
- single nucleotide variant
- Location
- chr13:23354728 (GRCh38)
- Gene constraint
- LOEUF 0.644 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Similar variants
- SACS c.2093+1G>A Likely pathogenic ★★ same condition
- SACS c.604+1G>A Likely pathogenic ★★ same condition
- SACS p.Ala4074Pro Pathogenic ★★ same condition
- SACS p.Arg1575Pro Pathogenic ★★ same condition
- SACS p.Arg1645Gln Likely pathogenic ★★ same condition
- SACS p.Arg1645Ter Pathogenic ★★ same condition
- SACS p.Arg1877Ter Pathogenic/Likely pathogenic ★★ same condition
- SACS p.Arg1907Ter Pathogenic ★★ same condition
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/sacs-p-pro628 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown