PDAP1

protein-coding

PDGFA associated protein 1

Gene summary

The protein encoded by this gene is a phosphoprotein that may upregulate the PDGFA-stimulated growth of fibroblasts and also downregulate the mitogenicity of PDGFB. The encoded protein in rodents has been shown to bind PDGFA with a low affinity. [provided by RefSeq, Dec 2010]

MANE transcript

NM_014891.7

Inheritance

—

ClinVar variants

U:15B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr7:99,392,048-99,408,597

External References & Databases

Ensembl (ENSG00000106244)

Transcript & Mutation Effects

hg38 • Region Span ~16.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PDAP1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 14

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014891.7. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			15 clinvar		1 clinvar	16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	0	1	16

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 43 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014891.7	RefSeq	NP_055706.1	6	MANE Select
ENST00000350498.8	Ensembl	ENSP00000222968.4	6	MANE Select
ENST00000426447.3	Ensembl	ENSP00000411287.1	3	Standard
ENST00000626285.1	Ensembl	ENSP00000486021.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Innate Immune System
Immune System

Biological Process

signal transduction
cell population proliferation
neutrophil degranulation

Molecular Function

RNA binding

Cellular Component

extracellular region
cytosol
plasma membrane
ficolin-1-rich granule lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000350498
Coding exons: 6
Length: 16782
Individuals with no LoFs: 125733
Homozygous LoFs: 1
Heterozygous LoFs: 13
Defined: 125747
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.37	71	112	0.635	0.00000717	1178
Missense (PolyPhen)		12	29.314	0.40936		319
Synonymous	-0.519	47	42.7	1.10	0.00000274	326
Loss of Function	2.02	4	11.4	0.352	5.78e-7	141

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00032	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Enhances PDGFA-stimulated cell growth in fibroblasts, but inhibits the mitogenic effect of PDGFB. {ECO:0000250}.;

Recessive Scores

pRec: 0.125

Intolerance Scores

LoFtool: 0.257
RVIS EVS: -0.32
RVIS percentile EVS: 31.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.824

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium