HPF1

histone PARylation factor 1

Basic information

Region (hg38): 4:169729470-169757944

Previous symbols: [ "C4orf27" ]

Links

ENSG00000056050 ∙ NCBI:54969 ∙ OMIM:616614 ∙ HGNC:26051 ∙ Uniprot:Q9NWY4 ∙ 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 HPF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HPF1 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			1	1		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	1	0

Variants in HPF1

This is a list of pathogenic ClinVar variants found in the HPF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-169729616-T-G		not specified	Uncertain significance (Aug 12, 2021)
4-169742096-G-A		not specified	Likely benign (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HPF1	protein_coding	protein_coding	ENST00000393381	8	28489

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000233	0.739	125472	1	273	125746	0.00109

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0576	166	168	0.988	0.00000777	2285
Missense in Polyphen		28	42.173	0.66393		593
Synonymous	0.535	54	59.2	0.912	0.00000290	605
Loss of Function	1.19	11	16.2	0.680	8.24e-7	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00147	0.00146
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000518	0.000508
European (Non-Finnish)	0.00143	0.00142
Middle Eastern	0.000109	0.000109
South Asian	0.00219	0.00209
Other	0.000656	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a cofactor for serine ADP-ribosylation by conferring serine specificity on PARP1 and PARP2: interacts with PARP1 and PARP1 and is able to change amino acid specificity toward serine (PubMed:28190768). Promotes histone serine ADP- ribosylation in response to DNA damage, limiting DNA damage- induced PARP1 hyper-automodification, and ensuring genome stability (PubMed:27067600, PubMed:28190768). {ECO:0000269|PubMed:27067600, ECO:0000269|PubMed:28190768}.

Recessive Scores

• pRec: 0.0814

Intolerance Scores

• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• pHI: 0.0709
• hipred: N
• hipred_score: 0.216
• ghis: 0.475

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Hpf1

Zebrafish Information Network

• Gene name: hpf1
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: increased curvature

Gene ontology

• Biological process: cellular response to DNA damage stimulus;regulation of protein ADP-ribosylation;peptidyl-serine ADP-ribosylation
• Cellular component: nucleus
• Molecular function: protein binding;zinc ion binding;histone binding;poly-ADP-D-ribose binding