Is PDGFB p.Arg149Ter (c.445C>T) pathogenic?

PDGFB p.Arg149Ter (c.445C>T) is classified Pathogenic in PDGFB (ClinVar, Multiple submitters, 7 submitters; last evaluated 2025-07-21). Absent from gnomAD v4.1; Associated with basal ganglia calcification, idiopathic, 5.

What condition is associated with PDGFB p.Arg149Ter (c.445C>T)?

PDGFB p.Arg149Ter (c.445C>T) is associated with basal ganglia calcification, idiopathic, 5 (ClinVar).

How common is PDGFB p.Arg149Ter (c.445C>T) in the general population?

PDGFB p.Arg149Ter (c.445C>T) is absent from gnomAD v4.1 (gnomAD).

How is Bilateral striopallidodentate calcinosis inherited?

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

PDGFB p.Arg149Ter

c.445C>T · rs397515633 · VCV75243

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,567,746)

Conditions

basal ganglia calcification, idiopathic, 5

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 4 of 7
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7	GERP 1.5, phastCons 1
Overall
CADD	42.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,567,746). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PDGFB
Protein: p.Arg149Ter
Coding: c.445C>T
MANE Select: NM_002608
dbSNP: rs397515633
Type: single nucleotide variant
Location: chr22:39231633 (GRCh38)
Gene constraint: LOEUF 0.473 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 73.77 · 6 PDB
Residue 149: a disulfide bond; a β-strand

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

Disease context

basal ganglia calcification, idiopathic, 5 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Bilateral striopallidodentate calcinosis (Orphanet):

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

Similar variants

PDGFB c.-318C>T Likely pathogenic ★ same condition
PDGFB c.-373C>G Likely pathogenic ★ same condition
PDGFB p.Gln145Ter Pathogenic ★ same condition
PDGFB p.Met1Val Likely pathogenic ★ same condition
PDGFB p.Arg100Cys Conflicting classifications of pathogenicity ★ ⚠ same condition
PDGFB p.Arg200Ter Conflicting classifications of pathogenicity ★ ⚠ same condition
PDGFB p.Arg216His Conflicting classifications of pathogenicity ★ ⚠ same condition
PDGFB p.Cys124Arg 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/pdgfb-p-arg149ter (accessed [today's date]).

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