PARPBP

PARP1 binding protein

Basic information

Region (hg38): 12:102120182-102197520

Previous symbols: [ "C12orf48" ]

Links

ENSG00000185480 ∙ NCBI:55010 ∙ OMIM:613687 ∙ HGNC:26074 ∙ Uniprot:Q9NWS1 ∙ 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 PARPBP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PARPBP 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				1		1
missense			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		1	3
Total	0	0	36	2	1

Variants in PARPBP

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

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

Position	Type	Phenotype	Significance	ClinVar
12-102123983-G-A		not specified	Uncertain significance (Mar 07, 2023)
12-102124006-G-T		not specified	Uncertain significance (Feb 06, 2023)
12-102124025-C-T		not specified	Uncertain significance (Aug 14, 2023)
12-102148338-T-A		not specified	Uncertain significance (Oct 17, 2023)
12-102148348-T-C		not specified	Uncertain significance (Feb 28, 2024)
12-102148387-T-C		not specified	Uncertain significance (Jun 26, 2023)
12-102148403-T-C			Likely benign (May 01, 2022)
12-102148410-C-A		not specified	Likely benign (Apr 07, 2023)
12-102148422-G-T		not specified	Uncertain significance (Feb 28, 2024)
12-102164510-G-A		not specified	Uncertain significance (Jun 07, 2023)
12-102164525-A-G		not specified	Uncertain significance (Apr 13, 2023)
12-102164534-G-A		not specified	Uncertain significance (Dec 07, 2021)
12-102164565-A-C		not specified	Uncertain significance (Jun 07, 2024)
12-102164591-C-G		not specified	Uncertain significance (May 20, 2024)
12-102164593-A-C		not specified	Uncertain significance (Jan 29, 2024)
12-102165753-A-G		not specified	Uncertain significance (Jul 20, 2021)
12-102165853-A-G		not specified	Uncertain significance (Mar 13, 2023)
12-102165854-T-A		not specified	Uncertain significance (May 31, 2023)
12-102165874-C-A		not specified	Uncertain significance (Sep 25, 2023)
12-102165882-A-C		not specified	Uncertain significance (Oct 12, 2021)
12-102175485-T-C		not specified	Uncertain significance (Apr 20, 2023)
12-102175515-A-G		not specified	Uncertain significance (Jan 30, 2024)
12-102175518-T-A		not specified	Uncertain significance (Apr 18, 2023)
12-102175658-C-G		not specified	Uncertain significance (Sep 01, 2021)
12-102175665-G-A		not specified	Uncertain significance (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PARPBP	protein_coding	protein_coding	ENST00000358383	10	77343

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.19e-16	0.00556	125283	4	444	125731	0.00178

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.331	306	290	1.05	0.0000137	3824
Missense in Polyphen		82	82.092	0.99888		1205
Synonymous	0.623	96	104	0.922	0.00000519	1063
Loss of Function	-0.149	24	23.2	1.03	0.00000110	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00138	0.00137
Ashkenazi Jewish	0.00	0.00
East Asian	0.0194	0.0185
Finnish	0.000609	0.000601
European (Non-Finnish)	0.000413	0.000405
Middle Eastern	0.0194	0.0185
South Asian	0.000416	0.000359
Other	0.000501	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required to suppress inappropriate homologous recombination, thereby playing a central role DNA repair and in the maintenance of genomic stability. Antagonizes homologous recombination by interfering with the formation of the RAD51-DNA homologous recombination structure. Binds single-strand DNA and poly(A) homopolymers. Positively regulate the poly(ADP- ribosyl)ation activity of PARP1; however such function may be indirect. {ECO:0000269|PubMed:20931645, ECO:0000269|PubMed:22153967}.

Recessive Scores

• pRec: 0.0848

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.85

Haploinsufficiency Scores

• pHI: 0.326
• hipred: N
• hipred_score: 0.170
• ghis: 0.453

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Parpbp

Gene ontology

• Biological process: DNA repair;negative regulation of double-strand break repair via homologous recombination
• Cellular component: chromatin;nucleoplasm;cytoplasm
• Molecular function: DNA binding;protein binding