SASH1 p.Pro13=
c.39T>C · VCV3904871
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00679%, sas)
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 -1.1 | GERP -2.3, phastCons 0.01 |
| Overall | ||
| CADD | 5.335 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00679%
South Asian · 6/88,380 alleles
Filtering AF
0.00293%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.002%
Overall
0.00172%
27/1,573,512 alleles · very rare
exomes 24/1,422,484 · genomes 3/151,028 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00679% | 14,730 |
| East Asian | 0.00459% | 21,773 |
| African / African-American | 0.00406% | 24,604 |
| Admixed American | 0.00176% | 56,662 |
| European (non-Finnish) | 0.00129% | 77,794 |
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.Pro13=
- Coding
- c.39T>C
- MANE Select
- NM_015278
- Type
- single nucleotide variant
- Location
- chr6:148343106 (GRCh38)
- Gene constraint
- LOEUF 0.412 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.90 · 2 PDB
- Residue 13
- the 'disordered' region
Similar variants
- 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
- SASH1 p.Asp1140= 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-pro13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown