PWP2

PWP2 small subunit processome component, the group of WD repeat domain containing|UTPb subcomplex

Basic information

Region (hg38): 21:44107372-44131181

Previous symbols: [ "PWP2H" ]

Links

ENSG00000241945 ∙ NCBI:5822 ∙ OMIM:601475 ∙ HGNC:9711 ∙ Uniprot:Q15269 ∙ 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 PWP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PWP2 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			67	2		69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	67	2	0

Variants in PWP2

This is a list of pathogenic ClinVar variants found in the PWP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-44108995-G-C		not specified	Uncertain significance (Dec 21, 2023)
21-44109012-G-A		not specified	Uncertain significance (Apr 24, 2024)
21-44109015-G-A		not specified	Uncertain significance (Jul 26, 2022)
21-44109039-A-G		not specified	Uncertain significance (Feb 12, 2024)
21-44109080-G-C		not specified	Uncertain significance (Jan 04, 2024)
21-44113773-C-T		not specified	Uncertain significance (Jun 30, 2022)
21-44113785-G-A		not specified	Uncertain significance (Mar 29, 2022)
21-44113815-C-T		not specified	Uncertain significance (Dec 06, 2023)
21-44113839-T-C		not specified	Uncertain significance (May 11, 2022)
21-44114188-C-T		not specified	Uncertain significance (Oct 05, 2021)
21-44114203-T-C		not specified	Uncertain significance (Dec 30, 2023)
21-44114206-T-C		not specified	Uncertain significance (Mar 27, 2023)
21-44114245-C-T		not specified	Uncertain significance (Aug 16, 2021)
21-44114650-A-C		not specified	Uncertain significance (Dec 20, 2021)
21-44114669-C-T		not specified	Uncertain significance (Jan 16, 2024)
21-44114671-C-T		not specified	Uncertain significance (Aug 02, 2023)
21-44114695-G-C		not specified	Uncertain significance (Nov 10, 2022)
21-44114744-G-A		not specified	Uncertain significance (Apr 20, 2024)
21-44114759-A-C		not specified	Uncertain significance (Jun 10, 2024)
21-44115358-G-A		not specified	Uncertain significance (Jul 27, 2021)
21-44115724-A-C		not specified	Uncertain significance (Feb 06, 2023)
21-44115773-C-T		not specified	Uncertain significance (May 14, 2024)
21-44115794-T-C		not specified	Uncertain significance (Jan 30, 2024)
21-44115838-G-A		not specified	Uncertain significance (Sep 13, 2023)
21-44115854-T-A		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PWP2	protein_coding	protein_coding	ENST00000291576	21	23893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000699	0.999	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.325	549	571	0.962	0.0000360	5989
Missense in Polyphen		162	187.6	0.86354		1995
Synonymous	-1.32	271	245	1.11	0.0000176	1820
Loss of Function	4.18	14	43.9	0.319	0.00000222	490

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000298	0.000297
Ashkenazi Jewish	0.000250	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000152	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.000240	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.456
• rvis_EVS: -0.56
• rvis_percentile_EVS: 19.07

Haploinsufficiency Scores

• pHI: 0.759
• hipred: Y
• hipred_score: 0.611
• ghis: 0.594

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pwp2

Zebrafish Information Network

• Gene name: pwp2h
• Affected structure: intestinal bulb epithelium
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: ribosomal small subunit assembly;maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing
• Cellular component: nucleoplasm;small-subunit processome;Pwp2p-containing subcomplex of 90S preribosome
• Molecular function: RNA binding