Is PDGFRA p.Ile548= (c.1644T>A) pathogenic?

PDGFRA p.Ile548= (c.1644T>A) is classified Benign/Likely benign in PDGFRA (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-30). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with PDGFRA p.Ile548= (c.1644T>A)?

PDGFRA p.Ile548= (c.1644T>A) is associated with hereditary neoplastic syndrome, gastrointestinal stromal tumor (ClinVar).

How common is PDGFRA p.Ile548= (c.1644T>A) in the general population?

PDGFRA p.Ile548= (c.1644T>A) is absent from gnomAD v4.1 (gnomAD).

PDGFRA p.Ile548=

c.1644T>A · rs115085731 · VCV1164432

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

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 0.055	GERP -2.1, phastCons 0.96
Overall
CADD	6.455	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PDGFRA
Protein: p.Ile548=
Coding: c.1644T>A
MANE Select: NM_006206
dbSNP: rs115085731
Type: single nucleotide variant
Location: chr4:54274616 (GRCh38)
Gene constraint: LOEUF 0.264 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 72.91 · 19 PDB

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: gastrointestinal stromal tumor

Similar variants

PDGFRA p.Ile548Val Uncertain significance ★★ ⚠ same residue
PDGFRA p.Ile548Phe Uncertain significance ★ ⚠ same residue
PDGFRA p.Ile548Thr Uncertain significance ★ ⚠ same residue
PDGFRA c.1364+3A>G Uncertain significance ★★ same condition
PDGFRA c.1364+4T>C Uncertain significance ★★ same condition
PDGFRA c.1787-5C>G Uncertain significance ★★ same condition
PDGFRA c.2002+2T>C Uncertain significance ★★ same condition
PDGFRA c.2002+4G>A Uncertain significance ★★ 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/pdgfra-p-ile548 (accessed [today's date]).

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