PDGFB p.Ala58=
c.174C>T · VCV4947919
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
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 -4.5 | GERP -3.1 |
| Overall | ||
| CADD | 1.867 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,016 alleles
Filtering AF
0.0025%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00219%
Overall
0.00309%
49/1,587,834 alleles · ultra-rare
exomes 43/1,435,672 · genomes 6/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,016 |
| Remaining individualsnot grpmax-eligible | 0.0065% | 15,381 |
| South Asian | 0.00344% | 29,032 |
| European (non-Finnish) | 0.00334% | 29,976 |
| Finnishnot grpmax-eligible | 0.00157% | 63,754 |
| African / African-American | 0.00137% | 72,914 |
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
- PDGFB
- Protein
- p.Ala58=
- Coding
- c.174C>T
- MANE Select
- NM_002608
- Type
- single nucleotide variant
- Location
- chr22:39233511 (GRCh38)
- Gene constraint
- LOEUF 0.473 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 73.77 · 6 PDB
Similar variants
- PDGFB p.Arg149Ter Pathogenic ★★ same type
- PDGFB c.64-5G>A Uncertain significance ★★ same type
- PDGFB p.Ala6Val Uncertain significance ★★ ⚠ same type
- PDGFB p.Arg142Cys Uncertain significance ★★ ⚠ same type
- PDGFB p.Arg160Trp Uncertain significance ★★ ⚠ same type
- PDGFB p.Arg187Gln Uncertain significance ★★ ⚠ same type
- PDGFB p.Arg187Trp Uncertain significance ★★ ⚠ same type
- PDGFB p.Arg207Gln 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/pdgfb-p-ala58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown