SARS1 p.Pro287=
c.861G>A · VCV3437376
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0977%, 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 -13 | GERP -3.3 |
| Overall | ||
| CADD | 0.237 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0977%
South Asian · 89/91,078 alleles
Filtering AF
0.0812%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0752%
Overall
0.0137%
221/1,614,064 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0977% | 1,023 |
| Finnishnot grpmax-eligible | 0.0656% | 1,524 |
| Admixed American | 0.0617% | 1,622 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,416 |
| African / African-American | 0.008% | 12,501 |
| European (non-Finnish) | 0.00339% | 29,500 |
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
- SARS1
- Protein
- p.Pro287=
- Coding
- c.861G>A
- MANE Select
- NM_006513
- Type
- single nucleotide variant
- Location
- chr1:109235323 (GRCh38)
- Gene constraint
- LOEUF 0.57 · pLI 0.41 (gnomAD)
- Structure
- AlphaFold pLDDT 93.48 · 9 PDB
- Residue 287
- a turn
Similar variants
- SARS1 p.Arg121Gln Uncertain significance ★★ ⚠ same type
- SARS1 p.Arg404Cys Uncertain significance ★★ ⚠ same type
- SARS1 c.288+9T>C Benign ★★ same type
- SARS1 c.970-22T>C Benign ★★ same type
- SARS1 p.Glu149= Benign ★★ same type
- SARS1 p.Gly387Glu Benign/Likely benign ★★ ⚠ same type
- SARS1 p.Leu297= Likely benign ★★ same type
- SARS1 c.447+1G>A Likely pathogenic ★ 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/sars1-p-pro287 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown