PDAP1

PDGFA associated protein 1

Basic information

Region (hg38): 7:99392048-99408597

Links

ENSG00000106244 ∙ NCBI:11333 ∙ OMIM:607075 ∙ HGNC:14634 ∙ Uniprot:Q13442 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDAP1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	7	0	2

Variants in PDAP1

This is a list of pathogenic ClinVar variants found in the PDAP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-99392651-G-A			Likely benign (Apr 16, 2024)
7-99392652-GC-G			Benign (Jun 20, 2024)
7-99392653-C-T			Likely benign (Jan 30, 2025)
7-99392657-C-T			Likely benign (Oct 31, 2022)
7-99392666-C-G			Likely benign (Jun 21, 2023)
7-99392684-T-G			Uncertain significance (Jul 18, 2021)
7-99392690-T-G			Uncertain significance (May 12, 2022)
7-99392694-G-C			Likely benign (Jan 27, 2025)
7-99392702-A-G			Uncertain significance (Mar 24, 2022)
7-99392702-A-T		Inborn genetic diseases	Uncertain significance (Jun 18, 2021)
7-99392706-C-T			Likely benign (Oct 16, 2023)
7-99392707-G-A			Uncertain significance (Dec 21, 2023)
7-99392709-C-T			Likely benign (Feb 08, 2022)
7-99392710-G-A		Inborn genetic diseases	Uncertain significance (Dec 16, 2023)
7-99392712-C-T		ARPC1B-related disorder	Benign (Jan 31, 2025)
7-99392713-G-A		Inborn genetic diseases	Uncertain significance (Jan 17, 2025)
7-99392715-G-A			Likely benign (Jul 21, 2024)
7-99392721-G-A		ARPC1B-related disorder	Likely benign (Jan 20, 2025)
7-99392734-G-A		Inborn genetic diseases	Uncertain significance (Nov 10, 2024)
7-99392742-G-C			Likely benign (Jul 13, 2024)
7-99392748-TC-T			Pathogenic (Jul 19, 2022)
7-99392760-C-A			Uncertain significance (Oct 22, 2021)
7-99392763-G-A			Likely benign (Jan 13, 2025)
7-99392768-G-A		Inborn genetic diseases	Uncertain significance (Nov 20, 2023)
7-99392772-C-T			Likely benign (Jul 04, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDAP1	protein_coding	protein_coding	ENST00000350498	6	16782

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0496	0.930	125733	1	13	125747	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	71	112	0.635	0.00000717	1178
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000380	0.000380
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Enhances PDGFA-stimulated cell growth in fibroblasts, but inhibits the mitogenic effect of PDGFB. {ECO:0000250}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.257
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.430
• hipred: Y
• hipred_score: 0.593
• ghis: 0.639

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdap1

Gene ontology

• Biological process: signal transduction;cell population proliferation;neutrophil degranulation
• Cellular component: extracellular region;cytosol;plasma membrane;ficolin-1-rich granule lumen
• Molecular function: RNA binding