Is PDGFRB p.Ser286= (c.858G>A) pathogenic?

PDGFRB p.Ser286= (c.858G>A) is classified Likely benign in PDGFRB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-09). Very rare (popmax 0.00988%, sas); Associated with basal ganglia calcification, idiopathic, 4.

How common is PDGFRB p.Ser286= (c.858G>A) in the general population?

PDGFRB p.Ser286= (c.858G>A) is very rare (popmax 0.00988%, sas) (gnomAD).

How is Bilateral striopallidodentate calcinosis inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

PDGFRB p.Ser286=

Q: What condition is associated with PDGFRB p.Ser286= (c.858G>A)?

PDGFRB p.Ser286= (c.858G>A) is associated with basal ganglia calcification, idiopathic, 4, acroosteolysis-keloid-like lesions-premature aging syndrome, skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome (ClinVar).

c.858G>A · rs778116813 · VCV740421

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00988%, sas)

Conditions

basal ganglia calcification, idiopathic, 4

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 -9.9	GERP -5
Overall
CADD	1.504	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00988% South Asian · 9/91,062 alleles

Filtering AF 0.00514% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00375%

Overall 0.00254% 41/1,613,708 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00988%	10,118
East Asian	0.00891%	11,218
African / African-American	0.00401%	24,937
Admixed American	0.00333%	29,991
Remaining individualsnot grpmax-eligible	0.0032%	31,240
European (non-Finnish)	0.00178%	56,184

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.Ser286=
Coding: c.858G>A
MANE Select: NM_002609
dbSNP: rs778116813
Type: single nucleotide variant
Location: chr5:150133662 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI 0.94 (gnomAD)
Structure: AlphaFold pLDDT 72.96 · 9 PDB
Residue 286: a disulfide bond; the ig-like c2-type 3 domain

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

Disease context

basal ganglia calcification, idiopathic, 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: acroosteolysis-keloid-like lesions-premature aging syndrome skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome infantile myofibromatosis

For Bilateral striopallidodentate calcinosis (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Not applicable
Onset: Adult

Similar variants

PDGFRB p.Arg561Cys Pathogenic ★★ ⚠ same condition
PDGFRB p.Asn666His Pathogenic/Likely pathogenic ★★ same condition
PDGFRB p.Asn666Lys Pathogenic/Likely pathogenic ★★ same condition
PDGFRB p.Asn666Ser Pathogenic/Likely pathogenic ★★ ⚠ same condition
PDGFRB p.Pro560Leu Pathogenic/Likely pathogenic ★★ same condition
PDGFRB p.Pro584Arg Pathogenic ★★ same condition
PDGFRB p.Trp566Arg Pathogenic ★★ same condition
PDGFRB p.Ala513Thr 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/pdgfrb-p-ser286 (accessed [today's date]).

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