Is PDGFB p.Ser19= (c.57C>T) pathogenic?

PDGFB p.Ser19= (c.57C>T) is classified Likely benign in PDGFB (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-11). Very rare (popmax 0.00034%, nfe).

How common is PDGFB p.Ser19= (c.57C>T) in the general population?

PDGFB p.Ser19= (c.57C>T) is very rare (popmax 0.00034%, nfe) (gnomAD).

PDGFB p.Ser19=

c.57C>T · rs1300554096 · VCV1597958

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00034%, nfe)

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 5.5	GERP 0.89, phastCons 1
Overall
CADD	17.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00034% European (non-Finnish) · 4/1,176,860 alleles

Filtering AF 8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000249% 4/1,606,432 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: PDGFB
Protein: p.Ser19=
Coding: c.57C>T
MANE Select: NM_002608
dbSNP: rs1300554096
Type: single nucleotide variant
Location: chr22:39243907 (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-ser19 (accessed [today's date]).

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