PWP1

PWP1 homolog, endonuclein, the group of WD repeat domain containing

Basic information

Region (hg38): 12:107685799-107713162

Links

ENSG00000136045 ∙ NCBI:11137 ∙ OMIM:620055 ∙ HGNC:17015 ∙ Uniprot:Q13610 ∙ 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 PWP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PWP1 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in PWP1

This is a list of pathogenic ClinVar variants found in the PWP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-107685907-G-C		not specified	Uncertain significance (Jan 23, 2025)
12-107688496-G-A		not specified	Uncertain significance (Feb 08, 2025)
12-107688682-C-T		not specified	Uncertain significance (May 15, 2024)
12-107688712-G-C		not specified	Uncertain significance (Dec 16, 2024)
12-107688736-A-G		not specified	Uncertain significance (Oct 06, 2023)
12-107688755-A-G		not specified	Uncertain significance (Mar 20, 2024)
12-107692850-C-T		not specified	Uncertain significance (Dec 03, 2024)
12-107692858-G-C		not specified	Uncertain significance (Aug 28, 2024)
12-107692873-G-T		not specified	Uncertain significance (Nov 03, 2022)
12-107693070-A-G		not specified	Uncertain significance (Jan 29, 2025)
12-107696542-G-A		not specified	Uncertain significance (Apr 25, 2022)
12-107696549-G-T		not specified	Uncertain significance (Jan 01, 2025)
12-107697494-C-T		not specified	Uncertain significance (Dec 03, 2024)
12-107697594-G-C		not specified	Uncertain significance (Jan 26, 2022)
12-107702952-C-T		not specified	Uncertain significance (May 09, 2023)
12-107702963-A-G		not specified	Uncertain significance (Feb 22, 2023)
12-107703027-A-G		not specified	Uncertain significance (Dec 03, 2024)
12-107704648-G-T		not specified	Uncertain significance (Apr 19, 2024)
12-107704676-C-T		not specified	Uncertain significance (Sep 06, 2022)
12-107704689-G-A		not specified	Uncertain significance (Nov 03, 2023)
12-107704730-T-C		not specified	Uncertain significance (Oct 17, 2023)
12-107708927-C-T		not specified	Uncertain significance (Jul 05, 2024)
12-107709119-C-G		not specified	Uncertain significance (Sep 14, 2021)
12-107710433-C-T		not specified	Uncertain significance (Feb 28, 2024)
12-107710505-C-T		not specified	Uncertain significance (Nov 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PWP1	protein_coding	protein_coding	ENST00000412830	15	27436

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.99e-12	0.607	125569	0	178	125747	0.000708

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	217	277	0.784	0.0000141	3311
Missense in Polyphen		49	70.546	0.69458		857
Synonymous	-0.0916	98	96.9	1.01	0.00000504	912
Loss of Function	1.51	23	32.3	0.713	0.00000169	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00515	0.00510
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000709	0.000707
Finnish	0.00	0.00
European (Non-Finnish)	0.000440	0.000440
Middle Eastern	0.000709	0.000707
South Asian	0.000700	0.000686
Other	0.000815	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Chromatin-associated factor that regulates transcription (PubMed:29065309). Regulates Pol I-mediated rRNA biogenesis and, probably, Pol III-mediated transcription (PubMed:29065309). Regulates the epigenetic status of rDNA (PubMed:29065309). {ECO:0000269|PubMed:29065309}.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase (Consensus)

Intolerance Scores

• loftool: 0.923
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.45

Haploinsufficiency Scores

• pHI: 0.503
• hipred: N
• hipred_score: 0.476
• ghis: 0.613

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.943

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pwp1
• Phenotype: hematopoietic system 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); immune system phenotype

Gene ontology

• Biological process: transcription, DNA-templated;negative regulation of peptidyl-serine phosphorylation of STAT protein;histone H4-K20 trimethylation;ribosome biogenesis;positive regulation of transcription of nucleolar large rRNA by RNA polymerase I;positive regulation of stem cell differentiation
• Cellular component: nucleus;chromosome;nucleolus;Golgi apparatus
• Molecular function: H4K20me3 modified histone binding