Is PDGFRB p.Pro27Ser (c.79C>T) pathogenic?

PDGFRB p.Pro27Ser (c.79C>T) is classified Uncertain significance in PDGFRB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-12). AlphaMissense: likely benign (0.0899); Very rare (popmax 0.00131%, nfe); Associated with Inborn genetic diseases.

What condition is associated with PDGFRB p.Pro27Ser (c.79C>T)?

PDGFRB p.Pro27Ser (c.79C>T) is associated with Inborn genetic diseases (ClinVar).

How common is PDGFRB p.Pro27Ser (c.79C>T) in the general population?

PDGFRB p.Pro27Ser (c.79C>T) is very rare (popmax 0.00131%, nfe) (gnomAD).

What do computational predictors say about PDGFRB p.Pro27Ser (c.79C>T)?

AlphaMissense predicts likely benign (score 0.0899) — an in-silico prediction, not a clinical call.

PDGFRB p.Pro27Ser

c.79C>T · VCV3930241

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0899 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00131%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0899	likely benign
REVEL	0.037	moderately benign-leaning
SaProt	LLR -6.47	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.28 · evaluated, not missing
Constraint at this position
Conservation	phyloP 3	GERP -3.3, phastCons 1
Regional constraint	o/e 0.79	unconstrained · MANE · 16 kb · p 5.4e-12 · regional, not allelic
Overall
CADD	16.32	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00131% European (non-Finnish) · 15/1,145,998 alleles

Filtering AF 0.000786% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000623%

Overall 0.000973% 15/1,542,306 alleles · very rare

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.Pro27Ser
Coding: c.79C>T
MANE Select: NM_002609
Type: single nucleotide variant
Location: chr5:150135840 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI 0.94 (gnomAD)
Structure: AlphaFold pLDDT 72.96 · 9 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PDGFRB p.Asn666His Pathogenic/Likely pathogenic ★★ same condition
PDGFRB p.Arg788Ter Uncertain significance ★★ same condition
PDGFRB p.Asn307Ser Uncertain significance ★★ ⚠ same condition
PDGFRB p.Asp1103Tyr Uncertain significance ★★ ⚠ same condition
PDGFRB p.Asp706Asn Uncertain significance ★★ ⚠ same condition
PDGFRB p.Leu24Phe Uncertain significance ★★ ⚠ same condition
PDGFRB p.Lys868Asn Uncertain significance ★★ ⚠ same condition
PDGFRB p.Met554Val 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-pro27ser (accessed [today's date]).

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