PUS1 p.Ser71=
c.213C>T · rs767305441 · VCV1108655
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00599%, sas)
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 0.93 | GERP 1, phastCons 0.18 |
| Overall | ||
| CADD | 9.723 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00599%
South Asian · 4/66,762 alleles
Filtering AF
0.002%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00114%
Overall
0.000551%
8/1,450,992 alleles · very rare
exomes 6/1,298,770 · genomes 2/152,222 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00599% | 16,691 |
| Remaining individualsnot grpmax-eligible | 0.00363% | 27,534 |
| Admixed American | 0.00268% | 37,246 |
| European (non-Finnish) | 9.06e-05% | 1,103,717 |
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
- PUS1
- Protein
- p.Ser71=
- Coding
- c.213C>T
- MANE Select
- NM_025215
- dbSNP
- rs767305441
- Type
- single nucleotide variant
- Location
- chr12:131930045 (GRCh38)
- Gene constraint
- LOEUF 1.161 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.80 · 6 PDB
- Residue 71
- the 'disordered' region
Similar variants
- PUS1 p.Gln101Ter Pathogenic/Likely pathogenic ★★ same type
- PUS1 p.Gln154Ter Pathogenic ★★ same type
- PUS1 p.Lys306Ter Pathogenic/Likely pathogenic ★★ same type
- PUS1 p.Trp15Ter Pathogenic/Likely pathogenic ★★ same type
- PUS1 p.Trp161Ter Pathogenic/Likely pathogenic ★★ same type
- PUS1 p.Ala226Thr Uncertain significance ★★ ⚠ same type
- PUS1 p.Ala309Val Uncertain significance ★★ ⚠ same type
- PUS1 p.Ala328Val 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/pus1-p-ser71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown