PUS7 p.Phe137=
c.411C>T · rs753851280 · VCV1695207
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0318%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.562 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.51 | GERP -0.96 |
| Overall | ||
| CADD | 8.022 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0318%
Admixed American · 19/59,662 alleles
Filtering AF
0.0208%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0173%
Overall
0.00199%
32/1,610,790 alleles · ultra-rare
exomes 29/1,458,712 · genomes 3/152,078 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0318% | 3,140 |
| East Asian | 0.00223% | 44,830 |
| European (non-Finnish) | 0.00102% | 98,183 |
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
- PUS7
- Protein
- p.Phe137=
- Coding
- c.411C>T
- MANE Select
- NM_019042
- dbSNP
- rs753851280
- Type
- single nucleotide variant
- Location
- chr7:105506261 (GRCh38)
- Gene constraint
- LOEUF 0.727 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.67 · 1 PDB
- Residue 137
- a β-strand
Similar variants
- PUS7 c.1399-1G>C Pathogenic/Likely pathogenic ★★ same type
- PUS7 p.Asp503Tyr Pathogenic/Likely pathogenic ★★ same type
- PUS7 p.Arg661His Uncertain significance ★★ ⚠ same type
- PUS7 p.Met104Val Uncertain significance ★★ ⚠ same type
- PUS7 p.Ser135Ala Uncertain significance ★★ ⚠ same type
- PUS7 p.Thr269Ala Uncertain significance ★★ ⚠ same type
- PUS7 c.585+43G>C Benign ★★ same type
- PUS7 c.842+44A>G 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/pus7-p-phe137 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown