Is PDGFRB p.Glu1069Ter (c.3205G>T) pathogenic?

PDGFRB p.Glu1069Ter (c.3205G>T) is classified Uncertain significance in PDGFRB (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-27). Absent from gnomAD v4.1.

How common is PDGFRB p.Glu1069Ter (c.3205G>T) in the general population?

PDGFRB p.Glu1069Ter (c.3205G>T) is absent from gnomAD v4.1 (gnomAD).

PDGFRB p.Glu1069Ter

c.3205G>T · VCV3774518

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,610,282)

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	escapes	premature termination codon in the last exon (23 of 23) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.2, 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 1,610,282). 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: PDGFRB
Protein: p.Glu1069Ter
Coding: c.3205G>T
MANE Select: NM_002609
Type: single nucleotide variant
Location: chr5:150115879 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI 0.94 (gnomAD)
Structure: AlphaFold pLDDT 72.96 · 9 PDB
Residue 1069: the 'disordered' region

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

Similar variants

PDGFRB p.Glu1069Lys Likely benign ★ ⚠ 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
PDGFRB p.Trp566Arg 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-glu1069ter (accessed [today's date]).

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