POLDIP2

protein-coding

DNA polymerase delta interacting protein 2

Gene summary

This gene encodes a protein that interacts with the DNA polymerase delta p50 subunit, as well as with proliferating cell nuclear antigen. The encoded protein maybe play a role in the ability of the replication fork to bypass DNA lesions. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

MANE transcript

NM_015584.5

Inheritance

—

ClinVar variants

U:9B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr17:28,346,633-28,357,527

External References & Databases

Ensembl (ENSG00000004142)

Transcript & Mutation Effects

hg38 • Region Span ~10.9 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 POLDIP2 variants in ClinVar

1 Conditions Cataloged

not providedTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015584.5. 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			3 clinvar		5 clinvar	8
missense			3 clinvar			3
nonsense						0
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	9	0	6	15

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 49 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015584.5	RefSeq	NP_056399.1	11	MANE Select
ENST00000540200.6	Ensembl	ENSP00000475924.2	11	MANE Select
NM_001290145.2	RefSeq	NP_001277074.1	11	Standard
ENST00000618887.2	Ensembl	ENSP00000477665.2	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of macroautophagy
positive regulation of mitotic cell cycle
mitochondrion morphogenesis

Molecular Function

DNA binding
protein binding

Cellular Component

nucleus
mitochondrion
mitochondrial nucleoid

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000540200
Coding exons: 12
Length: 10887
Individuals with no LoFs: 124626
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 124641
p: 0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.94	129	208	0.621	0.0000117	2329
Missense (PolyPhen)		26	64.935	0.4004		707
Synonymous	0.512	71	76.7	0.926	0.00000396	716
Loss of Function	3.44	5	22.7	0.221	0.00000121	239

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.00027	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000056	0.000056	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.124

Essentials

Indispensability pred.: E
Indispensability score: 0.970

Gene Damage Prediction

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