POLDIP3

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

Basic information

Region (hg38): 22:42583721-42614962

Links

ENSG00000100227 ∙ NCBI:84271 ∙ OMIM:611520 ∙ HGNC:23782 ∙ Uniprot:Q9BY77 ∙ 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 POLDIP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLDIP3 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			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	0

Variants in POLDIP3

This is a list of pathogenic ClinVar variants found in the POLDIP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-42585809-T-A		not specified	Uncertain significance (Mar 19, 2024)
22-42585834-G-A		not specified	Uncertain significance (Mar 07, 2025)
22-42585873-G-C		not specified	Uncertain significance (Aug 11, 2024)
22-42585900-G-A		not specified	Uncertain significance (Sep 22, 2023)
22-42585922-G-A		not specified	Uncertain significance (Jan 08, 2025)
22-42585937-C-T		not specified	Uncertain significance (Nov 14, 2024)
22-42587554-T-C		not specified	Uncertain significance (Sep 16, 2021)
22-42591999-T-C		not specified	Uncertain significance (Nov 10, 2022)
22-42592067-A-C		not specified	Uncertain significance (Jun 21, 2022)
22-42595578-C-T		not specified	Uncertain significance (Dec 15, 2022)
22-42596219-C-G		not specified	Uncertain significance (Feb 13, 2025)
22-42596243-G-C		not specified	Uncertain significance (Feb 13, 2024)
22-42596250-A-G		not specified	Uncertain significance (Jun 09, 2022)
22-42596262-C-T		not specified	Uncertain significance (Mar 24, 2023)
22-42596275-G-A		not specified	Uncertain significance (Sep 08, 2024)
22-42596290-T-A		not specified	Uncertain significance (Jun 23, 2023)
22-42596295-G-A		not specified	Uncertain significance (May 03, 2023)
22-42596297-A-T		not specified	Uncertain significance (Oct 06, 2024)
22-42596317-T-C		not specified	Uncertain significance (Nov 17, 2022)
22-42599699-A-T		not specified	Uncertain significance (Dec 27, 2023)
22-42599706-G-A		not specified	Uncertain significance (Feb 25, 2025)
22-42599715-C-T		not specified	Likely benign (Aug 30, 2022)
22-42599726-G-A		not specified	Uncertain significance (Oct 06, 2021)
22-42599742-T-C		not specified	Uncertain significance (Apr 18, 2023)
22-42599744-G-A		not specified	Uncertain significance (Dec 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLDIP3	protein_coding	protein_coding	ENST00000252115	9	31242

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.118	0.882	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.122	247	252	0.978	0.0000142	2729
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Transport of Mature mRNA derived from an Intron-Containing Transcript;mTOR signaling pathway;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Intolerance Scores

• loftool: 0.0622
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.52

Haploinsufficiency Scores

• pHI: 0.122
• hipred: Y
• hipred_score: 0.701
• ghis: 0.562

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.993

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Poldip3

Gene ontology

• Biological process: RNA export from nucleus;mRNA export from nucleus;poly(A)+ mRNA export from nucleus;mRNA 3'-end processing;positive regulation of translation
• Cellular component: transcription export complex;nucleoplasm;cytoplasm;cytosol;nuclear speck;cytoplasmic ribonucleoprotein granule
• Molecular function: RNA binding;protein binding;protein-containing complex binding