Is PDGFA p.Arg170= (c.510G>A) pathogenic?

PDGFA p.Arg170= (c.510G>A) is classified Benign in PDGFA (ClinVar, Single submitter, 1 submitter; last evaluated 2018-03-02). Low-frequency (popmax 4.11%, afr).

How common is PDGFA p.Arg170= (c.510G>A) in the general population?

PDGFA p.Arg170= (c.510G>A) is low-frequency (popmax 4.11%, afr) (gnomAD).

PDGFA p.Arg170=

c.510G>A · rs61733314 · VCV785203

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 4.11%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.065	moderately benign-leaning
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.51 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.4	GERP -1.1, phastCons 1
Overall
CADD	12.21	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 4.11% African / African-American · 3,088/75,064 alleles

Filtering AF 3.99% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.94%

Overall 0.216% 3,489/1,614,224 alleles · low-frequency exomes 1,684/1,461,856 · genomes 1,805/152,368 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	4.11%	24
Remaining individualsnot grpmax-eligible	0.32%	313
Admixed American	0.248%	403
Middle Eastern	0.165%	606
South Asian	0.00549%	18,217
European (non-Finnish)	0.00305%	32,779
East Asian	0.00223%	44,884

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: PDGFA
Protein: p.Arg170=
Coding: c.510G>A
MANE Select: NM_033023
dbSNP: rs61733314
Type: single nucleotide variant
Location: chr7:501186 (GRCh38)
Gene constraint: LOEUF 0.364 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 78.03 · 1 PDB
Residue 170: a β-strand

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

Similar variants

PDGFA c.580+620G>A Uncertain significance ★ ⚠ same type
PDGFA c.580+632C>T Uncertain significance ★ ⚠ same type
PDGFA c.580+643C>T Uncertain significance ★ ⚠ same type
PDGFA c.580+644G>A Uncertain significance ★ ⚠ same type
PDGFA p.Arg148Cys Uncertain significance ★ ⚠ same type
PDGFA p.Arg189Trp Uncertain significance ★ ⚠ same type
PDGFA p.Arg78Trp Uncertain significance ★ ⚠ same type
PDGFA p.Gln37His 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/pdgfa-p-arg170 (accessed [today's date]).

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