Is PDGFRB p.Arg511His (c.1532G>A) pathogenic?

PDGFRB p.Arg511His (c.1532G>A) is classified Uncertain significance in PDGFRB (ClinVar, Single submitter, 1 submitter; last evaluated 2026-03-03). AlphaMissense: likely benign (0.0583); Very rare (popmax 0.00668%, eas).

How common is PDGFRB p.Arg511His (c.1532G>A) in the general population?

PDGFRB p.Arg511His (c.1532G>A) is very rare (popmax 0.00668%, eas) (gnomAD).

What do computational predictors say about PDGFRB p.Arg511His (c.1532G>A)?

AlphaMissense predicts likely benign (score 0.0583) — an in-silico prediction, not a clinical call.

PDGFRB p.Arg511His

c.1532G>A · VCV4847506

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0583 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00668%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0583	likely benign
REVEL	0.129	moderately benign-leaning
SaProt	LLR -8.08	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.043	GERP -4.2, phastCons 0.85
Regional constraint	o/e 0.79	unconstrained · MANE · 16 kb · p 5.4e-12 · regional, not allelic
Overall
CADD	16.25	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00668% East Asian · 3/44,894 alleles

Filtering AF 0.00177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000891%

Overall 0.000958% 14/1,461,608 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00668%	14,965
South Asian	0.00329%	30,363
Remaining individualsnot grpmax-eligible	0.0016%	62,506
European (non-Finnish)	0.000593%	168,574

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.Arg511His
Coding: c.1532G>A
MANE Select: NM_002609
Type: single nucleotide variant
Location: chr5:150129804 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI 0.94 (gnomAD)
Structure: AlphaFold pLDDT 72.96 · 9 PDB
Residue 511: the ig-like c2-type 5 domain

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

Similar variants

PDGFRB p.Arg511Cys Uncertain significance ★ ⚠ same residue
PDGFRB p.Arg561Cys Pathogenic ★★ ⚠ same type
PDGFRB p.Asn666His Pathogenic/Likely pathogenic ★★ same type
PDGFRB p.Asn666Lys Pathogenic/Likely pathogenic ★★ same type
PDGFRB p.Asn666Ser Pathogenic/Likely pathogenic ★★ same type
PDGFRB p.Pro560Leu Pathogenic/Likely pathogenic ★★ same type
PDGFRB p.Pro584Arg Pathogenic ★★ same type
PDGFRB p.Trp566Arg 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/pdgfrb-p-arg511his (accessed [today's date]).

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