POLDIP3

protein-coding

DNA polymerase delta interacting protein 3, the group of RNA binding motif containing

Gene summary

This gene encodes an RRM (RNA recognition motif)-containing protein that participates in the regulation of translation by recruiting ribosomal protein S6 kinase beta-1 to mRNAs. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

MANE transcript

NM_032311.5

Inheritance

—

ClinVar variants

U:62B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr22:42,583,721-42,614,962

External References & Databases

Ensembl (ENSG00000100227)

Transcript & Mutation Effects

hg38 • Region Span ~31.2 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 POLDIP3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 59

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032311.5. 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			2 clinvar			2
missense			58 clinvar	3 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	62	3	0	65

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 42 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032311.5	RefSeq	NP_115687.2	9	MANE Select
ENST00000252115.10	Ensembl	ENSP00000252115.5	9	MANE Select
NM_001278657.2	RefSeq	NP_001265586.1	9	Standard
NM_001363052.2	RefSeq	NP_001349981.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
RNA Polymerase II Transcription
Metabolism of RNA
Cleavage of Growing Transcript in the Termination Region
RNA Polymerase II Transcription Termination

Biological Process

RNA export from nucleus
mRNA export from nucleus
poly(A)+ mRNA export from nucleus
mRNA 3'-end processing
positive regulation of translation

Molecular Function

RNA binding
protein binding
protein-containing complex binding

Cellular Component

transcription export complex
nucleoplasm
cytoplasm
cytosol
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000252115
Coding exons: 9
Length: 31242
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125748
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.122	247	252	0.978	0.0000142	2729
Missense (PolyPhen)		78	105.99	0.73591		1114
Synonymous	-0.656	105	96.8	1.08	0.00000516	880
Loss of Function	3.24	6	22.6	0.265	0.00000155	216

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000053	0.000044	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Is involved in regulation of translation. Is preferentially associated with CBC-bound spliced mRNA-protein complexes during the pioneer round of mRNA translation. Contributes to enhanced translational efficiency of spliced over nonspliced mRNAs. Recruits activated ribosomal protein S6 kinase beta-1 I/RPS6KB1 to newly synthesized mRNA. Involved in nuclear mRNA export; probably mediated by association with the TREX complex. {ECO:0000269|PubMed:18423201, ECO:0000269|PubMed:22928037}.;

Intolerance Scores

LoFtool: 0.0622
RVIS EVS: 0.26
RVIS percentile EVS: 70.52

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.993

Gene Damage Prediction

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