What condition is associated with PDGFRB p.Val34= (c.102C>T)?

PDGFRB p.Val34= (c.102C>T) is associated with skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome, myeloproliferative disorder, chronic, with eosinophilia, myofibromatosis, infantile, 1 (ClinVar).

PDGFRB p.Val34=

Q: Is PDGFRB p.Val34= (c.102C>T) pathogenic?

PDGFRB p.Val34= (c.102C>T) is classified Benign in PDGFRB (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-01). Common (popmax 6.26%, amr) — too common for a highly-penetrant pathogenic allele; Associated with skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome.

Q: How common is PDGFRB p.Val34= (c.102C>T) in the general population?

PDGFRB p.Val34= (c.102C>T) is common (popmax 6.26%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.102C>T · rs17708515 · VCV473399

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 6.26%, amr) — too common for a highly-penetrant pathogenic allele

Conditions

skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome

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 3.7	GERP -0.23, phastCons 1
Overall
CADD	13.44	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.26% Admixed American · 3,465/55,386 alleles

Filtering AF 6.08% ClinGen BA1/BS1 input FAF95, joint · FAF99 6.01%

Overall 0.742% 11,713/1,579,558 alleles · common

Ancestry group	Frequency	1 in
Admixed Americangrpmax	6.26%	16
South Asian	5.02%	20
East Asian	2.58%	39
Finnishnot grpmax-eligible	1.52%	66
Remaining individualsnot grpmax-eligible	1.13%	89
African / African-American	0.968%	103
Middle Eastern	0.307%	326
European (non-Finnish)	0.0407%	2,455

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.Val34=
Coding: c.102C>T
MANE Select: NM_002609
dbSNP: rs17708515
Type: single nucleotide variant
Location: chr5:150135817 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI 0.94 (gnomAD)
Structure: AlphaFold pLDDT 72.96 · 9 PDB
Residue 34: the ig-like c2-type 1 domain

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

Disease context

skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: myeloproliferative disorder, chronic, with eosinophilia myofibromatosis, infantile, 1 acroosteolysis-keloid-like lesions-premature aging syndrome basal ganglia calcification, idiopathic, 4 infantile myofibromatosis

Similar variants

PDGFRB p.Arg561Cys Pathogenic ★★ ⚠ same condition
PDGFRB p.Asn666His Pathogenic/Likely pathogenic ★★ same condition
PDGFRB p.Asn666Lys Pathogenic/Likely pathogenic ★★ same condition
PDGFRB p.Asn666Ser Pathogenic/Likely pathogenic ★★ same condition
PDGFRB p.Pro560Leu Pathogenic/Likely pathogenic ★★ same condition
PDGFRB p.Pro584Arg Pathogenic ★★ same condition
PDGFRB p.Trp566Arg Pathogenic ★★ same condition
PDGFRB p.Ala513Thr 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-val34 (accessed [today's date]).

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