PDGFD

Chr 11

platelet derived growth factor D

Also known as: IEGF, MSTP036, SCDGF-B, SCDGFB

NCBI Gene: 80310 ENSG00000170962 UniProt: Q9GZP0 OMIM: 609673

The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of this family are mitogenic factors for cells of mesenchymal origin and are characterized by a core motif of eight cysteines, seven of which are found in this factor. This gene product only forms homodimers and, therefore, does not dimerize with the other three family members. It differs from alpha and beta members of this family in having an unusual N-terminal domain, the CUB domain. Two splice variants have been identified for this gene. [provided by RefSeq, Jul 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

Clinical highlights

Gene–disease validity (ClinGen)

Limited · pulmonary arterial hypertension · AD · ClinGen 2022

not for standalone diagnostic reporting

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.73

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.73LOEUF

pLI 0.002

Z-score 2.46

OE 0.40 (0.24–0.73)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.34Z-score

OE missense 0.93 (0.83–1.05)

199 obs / 213.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.40 (0.24–0.73)

0≤0.351.4

Missense OE?0.93 (0.83–1.05)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 8 / 19.8Missense obs/exp: 199 / 213.1Syn Z: -0.02

Background carrier burden — how many people carry a rare variant somewhere in PDGFD?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 140

552 rare PASS variants

Rare truncating (LoF)

1 in 2,100

74 rare PASS variants

Rare synonymous (reference)

1 in 230

185 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PDGFD. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 140	1 in 3,100
South Asian	~43k	1 in 110	1 in 980
Remaining (unassigned)	~30k	1 in 95	1 in 1,900
European (Finnish)	~27k	1 in 590	1 in 5,300
Admixed American	~22k	1 in 84	1 in 1,600
African / African American	~21k	1 in 94	1 in 2,400
East Asian	~20k	1 in 68	1 in 980
Ashkenazi Jewish	~13k	1 in 360	≈ 1 in 6,500
Middle Eastern	~2,884	1 in 75	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 7 coding exons well covered in gnomAD exomes and genomes.? see exons ↓