Is PDGFRB p.Pro345= (c.1035G>A) pathogenic?

PDGFRB p.Pro345= (c.1035G>A) is classified Likely benign in PDGFRB (ClinVar, Single submitter, 1 submitter; last evaluated 2018-07-25). Very rare (popmax 0.00776%, sas).

How common is PDGFRB p.Pro345= (c.1035G>A) in the general population?

PDGFRB p.Pro345= (c.1035G>A) is very rare (popmax 0.00776%, sas) (gnomAD).

PDGFRB p.Pro345=

c.1035G>A · rs55889271 · VCV719190

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00776%, sas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.014	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -6.8	GERP -4.4
Overall
CADD	3.22	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00776% South Asian · 7/90,254 alleles

Filtering AF 0.00362% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0026%

Overall 0.00366% 59/1,610,122 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00802%	12,463
South Asiangrpmax	0.00776%	12,893
European (non-Finnish)	0.00382%	26,190
Ashkenazi Jewishnot grpmax-eligible	0.00339%	29,530
African / African-American	0.00134%	74,882

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Pro345=
Coding: c.1035G>A
MANE Select: NM_002609
dbSNP: rs55889271
Type: single nucleotide variant
Location: chr5:150132842 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI 0.94 (gnomAD)
Structure: AlphaFold pLDDT 72.96 · 9 PDB
Residue 345: a UniProt-annotated variant site (in); the ig-like c2-type 4 domain

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

Similar variants

PDGFRB p.Pro345Ser Benign/Likely benign ★★ same residue
PDGFRB p.Pro345Leu 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

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-pro345 (accessed [today's date]).

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