Is PDGFRB p.Val84= (c.252G>A) pathogenic?

PDGFRB p.Val84= (c.252G>A) is classified Likely benign in PDGFRB (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-10). Very rare (popmax 0.000254%, nfe); Associated with PDGFRB-related disorder.

What condition is associated with PDGFRB p.Val84= (c.252G>A)?

PDGFRB p.Val84= (c.252G>A) is associated with PDGFRB-related disorder (ClinVar).

How common is PDGFRB p.Val84= (c.252G>A) in the general population?

PDGFRB p.Val84= (c.252G>A) is very rare (popmax 0.000254%, nfe) (gnomAD).

PDGFRB p.Val84=

c.252G>A · rs140893382 · VCV3041297

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

Conditions

PDGFRB-related disorder

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 -0.65	GERP -4.2
Overall
CADD	2.509	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,179,912 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000186% 3/1,613,938 alleles · very rare

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: PDGFRB
Protein: p.Val84=
Coding: c.252G>A
MANE Select: NM_002609
dbSNP: rs140893382
Type: single nucleotide variant
Location: chr5:150135667 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI 0.94 (gnomAD)
Structure: AlphaFold pLDDT 72.96 · 9 PDB
Residue 84: a disulfide bond; the ig-like c2-type 1 domain; a β-strand

Full PDGFRB gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PDGFRB-related disorder

Similar variants

PDGFRB p.Val84Ala Uncertain significance ★ ⚠ same residue
PDGFRB p.Val84Glu Uncertain significance ★ ⚠ same residue
PDGFRB p.Val84Met Benign ★ same residue
PDGFRB p.Arg604Cys Uncertain significance ★★ ⚠ same condition
PDGFRB p.Glu563Lys Uncertain significance ★★ ⚠ same condition
PDGFRB p.Ser952Cys Uncertain significance ★★ ⚠ same condition
PDGFRB p.Lys567Glu Likely pathogenic ★ same condition
PDGFRB p.Val665Ala Pathogenic ★ same condition

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/pdgfrb-p-val84 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown