STAR p.Val125=
c.375G>A · rs1256051149 · VCV1081708
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, 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 0.23 | GERP -1.9, phastCons 0.009 |
| Overall | ||
| CADD | 6.594 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
East Asian · 5/44,880 alleles
Filtering AF
0.00435%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.000496%
8/1,614,146 alleles · ultra-rare
exomes 4/1,461,852 · genomes 4/152,294 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0111% | 8,976 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,504 |
| South Asian | 0.0011% | 91,084 |
| European (non-Finnish) | 8.47e-05% | 1,180,036 |
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
- STAR
- Protein
- p.Val125=
- Coding
- c.375G>A
- MANE Select
- NM_000349
- dbSNP
- rs1256051149
- Type
- single nucleotide variant
- Location
- chr8:38146379 (GRCh38)
- Gene constraint
- LOEUF 1.297 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.71 · 4 PDB
- Residue 125
- a β-strand; the start domain
Similar variants
- STAR p.Val125Met Uncertain significance ★ ⚠ same residue
- STAR c.178+1G>C Likely pathogenic ★★ same type
- STAR c.306+1G>A Likely pathogenic ★★ same type
- STAR c.307-1G>C Likely pathogenic ★★ same type
- STAR c.465+2T>C Pathogenic/Likely pathogenic ★★ same type
- STAR c.64+1G>A Pathogenic/Likely pathogenic ★★ same type
- STAR c.64+1G>T Pathogenic ★★ same type
- STAR p.Ala218Val 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/star-p-val125 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown