SASH1 p.Pro488=
c.1464G>A · rs150728102 · VCV3053806
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.249%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.5 | GERP -2.5 |
| Overall | ||
| CADD | 0.572 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.249%
East Asian · 102/40,986 alleles
Filtering AF
0.21%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.195%
Overall
0.0314%
489/1,558,910 alleles · rare
exomes 434/1,406,766 · genomes 55/152,144 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.249% | 402 |
| Middle Eastern | 0.103% | 975 |
| Finnishnot grpmax-eligible | 0.0729% | 1,371 |
| Remaining individualsnot grpmax-eligible | 0.0418% | 2,391 |
| European (non-Finnish) | 0.0247% | 4,052 |
| African / African-American | 0.0208% | 4,819 |
| Admixed American | 0.0112% | 8,936 |
| South Asian | 0.0048% | 20,849 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00354% | 28,264 |
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
- SASH1
- Protein
- p.Pro488=
- Coding
- c.1464G>A
- MANE Select
- NM_015278
- dbSNP
- rs150728102
- Type
- single nucleotide variant
- Location
- chr6:148531561 (GRCh38)
- Gene constraint
- LOEUF 0.412 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.90 · 2 PDB
- Residue 488
- the 'disordered' region
Similar variants
- SASH1 p.Pro488Leu Uncertain significance ★ ⚠ same residue
- SASH1 p.Arg811Gln Uncertain significance ★★ ⚠ same type
- SASH1 p.Lys134Ile Uncertain significance ★★ ⚠ same type
- SASH1 p.Pro984Leu Uncertain significance ★★ same type
- SASH1 p.Thr460Met Uncertain significance ★★ ⚠ same type
- SASH1 c.337-38G>C Benign ★★ same type
- SASH1 p.Arg1089Gln Benign/Likely benign ★★ same type
- SASH1 p.Arg820Gln Benign/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/sash1-p-pro488 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown