POLDIP2

DNA polymerase delta interacting protein 2

Basic information

Region (hg38): 17:28346633-28357527

Links

ENSG00000004142 ∙ NCBI:26073 ∙ OMIM:611519 ∙ HGNC:23781 ∙ Uniprot:Q9Y2S7 ∙ 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 POLDIP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POLDIP2 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					5	5
missense				1		1
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					3	3
Total	0	0	0	1	9

Variants in POLDIP2

This is a list of pathogenic ClinVar variants found in the POLDIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-28348239-C-T			Benign (Dec 31, 2019)
17-28349133-C-T			Benign (Dec 31, 2019)
17-28349157-T-C			Benign (Dec 31, 2019)
17-28352988-G-C			Benign (Dec 31, 2019)
17-28357257-GT-G			Benign (Apr 10, 2019)
17-28357342-G-A			Likely benign (Apr 09, 2019)
17-28357347-G-A			Benign (Dec 31, 2019)
17-28357364-G-GC			Benign (Jun 20, 2019)
17-28357368-T-G			Benign (Jul 27, 2018)
17-28357424-C-C			Benign (Jul 27, 2018)
17-28357504-G-GGC			Benign (May 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POLDIP2	protein_coding	protein_coding	ENST00000540200	12	10887

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.414	0.586	124626	0	15	124641	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	129	208	0.621	0.0000117	2329
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000331	0.000330
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000562	0.0000556
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.0000179	0.0000177
Middle Eastern	0.0000562	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.124

Haploinsufficiency Scores

• pHI: 0.187
• hipred: Y
• hipred_score: 0.639

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Poldip2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of macroautophagy;positive regulation of mitotic cell cycle;mitochondrion morphogenesis
• Cellular component: nucleus;mitochondrion;mitochondrial nucleoid
• Molecular function: DNA binding;protein binding