PDGFB p.Val151=
c.453C>G · rs55634318 · VCV1188397
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.82%, afr)
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 -0.28 | GERP -1.4, phastCons 0.083 |
| Overall | ||
| CADD | 1.612 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.82%
African / African-American · 2,825/73,954 alleles
Filtering AF
3.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.65%
Overall
1.37%
21,385/1,562,296 alleles · low-frequency
exomes 18,377/1,409,986 · genomes 3,008/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.82% | 26 |
| Amishnot grpmax-eligible | 2.97% | 34 |
| Middle Eastern | 1.7% | 59 |
| South Asian | 1.6% | 63 |
| Remaining individualsnot grpmax-eligible | 1.5% | 67 |
| Admixed American | 1.3% | 77 |
| European (non-Finnish) | 1.3% | 77 |
| Ashkenazi Jewishnot grpmax-eligible | 0.772% | 130 |
| Finnishnot grpmax-eligible | 0.451% | 222 |
| East Asian | 0.00709% | 14,107 |
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.Val151=
- Coding
- c.453C>G
- MANE Select
- NM_002608
- dbSNP
- rs55634318
- Type
- single nucleotide variant
- Location
- chr22:39231625 (GRCh38)
- Gene constraint
- LOEUF 0.473 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 73.77 · 6 PDB
- Residue 151
- a β-strand
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-val151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown