Is PDGFB p.Ser10Phe (c.29C>T) pathogenic?

PDGFB p.Ser10Phe (c.29C>T) is classified Uncertain significance in PDGFB (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-26). AlphaMissense: likely benign (0.1971); Very rare (popmax 0.00227%, eas).

How common is PDGFB p.Ser10Phe (c.29C>T) in the general population?

PDGFB p.Ser10Phe (c.29C>T) is very rare (popmax 0.00227%, eas) (gnomAD).

What do computational predictors say about PDGFB p.Ser10Phe (c.29C>T)?

AlphaMissense predicts likely benign (score 0.1971) — an in-silico prediction, not a clinical call.

PDGFB p.Ser10Phe

c.29C>T · rs200943853 · VCV2788081

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1971 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00227%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1971	likely benign
REVEL	0.162	moderately benign-leaning
SaProt	LLR -7.43	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.2	GERP -0.2, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 18 kb · p 0.021 · regional, not allelic
Overall
CADD	20.8	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 0.00227% East Asian · 1/43,984 alleles

Overall 6.25e-05% 1/1,600,112 alleles · very rare exomes 1/1,448,138 · genomes 0/151,974 · joint denominator

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: PDGFB
Protein: p.Ser10Phe
Coding: c.29C>T
MANE Select: NM_002608
dbSNP: rs200943853
Type: single nucleotide variant
Location: chr22:39243935 (GRCh38)
Gene constraint: LOEUF 0.473 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 73.77 · 6 PDB

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

Similar variants

PDGFB p.Arg149Ter Pathogenic ★★ same type
PDGFB c.64-5G>A Uncertain significance ★★ same type
PDGFB p.Ala6Val Uncertain significance ★★ ⚠ same type
PDGFB p.Arg142Cys Uncertain significance ★★ ⚠ same type
PDGFB p.Arg160Trp Uncertain significance ★★ ⚠ same type
PDGFB p.Arg187Gln Uncertain significance ★★ ⚠ same type
PDGFB p.Arg187Trp Uncertain significance ★★ ⚠ same type
PDGFB p.Arg207Gln Uncertain significance ★★ ⚠ 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/pdgfb-p-ser10phe (accessed [today's date]).

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