GeneBe

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.

  • not_specified (46 variants)
  • not_provided (1 variants)

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. These statistics are base on transcript: NM_000007062.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
46
clinvar
 46
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 46 0 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PWP1protein_codingprotein_codingENST00000412830 1527436
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.99e-120.60712556901781257470.000708
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.282172770.7840.00001413311
Missense in Polyphen4970.5460.69458857
Synonymous-0.09169896.91.010.00000504912
Loss of Function1.512332.30.7130.00000169363

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.005150.00510
Ashkenazi Jewish0.00009930.0000992
East Asian0.0007090.000707
Finnish0.000.00
European (Non-Finnish)0.0004400.000440
Middle Eastern0.0007090.000707
South Asian0.0007000.000686
Other0.0008150.000815

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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