PPWD1

peptidylprolyl isomerase domain and WD repeat containing 1, the group of Cyclophilin peptidylprolyl isomerases|Spliceosomal C complex|Spliceosomal P complex|WD repeat domain containing

Basic information

Region (hg38): 5:65563235-65587549

Links

ENSG00000113593 ∙ NCBI:23398 ∙ OMIM:618274 ∙ HGNC:28954 ∙ Uniprot:Q96BP3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PPWD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPWD1 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			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in PPWD1

This is a list of pathogenic ClinVar variants found in the PPWD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-65563318-C-T		not specified	Uncertain significance (Jul 25, 2023)
5-65563329-A-G		not specified	Uncertain significance (May 06, 2024)
5-65563357-G-A		not specified	Uncertain significance (Sep 08, 2023)
5-65563375-C-T		not specified	Uncertain significance (Jun 05, 2023)
5-65563426-C-T		not specified	Uncertain significance (Jan 04, 2024)
5-65563440-G-C		not specified	Uncertain significance (Sep 20, 2023)
5-65567570-G-A		not specified	Uncertain significance (Dec 03, 2021)
5-65567603-T-G		not specified	Uncertain significance (Feb 26, 2024)
5-65569721-G-A		not specified	Uncertain significance (Aug 02, 2022)
5-65569919-T-G		not specified	Uncertain significance (Jun 30, 2023)
5-65571868-A-G		not specified	Uncertain significance (Jan 19, 2022)
5-65572172-C-G		not specified	Uncertain significance (May 05, 2023)
5-65572173-G-A		not specified	Likely benign (Jul 06, 2022)
5-65572261-T-G		not specified	Uncertain significance (Sep 16, 2021)
5-65572275-G-A		not specified	Uncertain significance (Jul 05, 2023)
5-65576952-G-C		not specified	Uncertain significance (Jun 07, 2024)
5-65576991-T-C		not specified	Uncertain significance (Feb 27, 2024)
5-65577003-A-G		not specified	Uncertain significance (May 15, 2024)
5-65579483-A-G		not specified	Uncertain significance (Jan 26, 2023)
5-65579518-A-G		not specified	Uncertain significance (Apr 07, 2022)
5-65579527-A-G		not specified	Uncertain significance (Mar 20, 2023)
5-65579575-A-G		not specified	Uncertain significance (Mar 01, 2023)
5-65583063-C-T		not specified	Uncertain significance (Jan 04, 2024)
5-65583122-A-G		not specified	Uncertain significance (Aug 01, 2022)
5-65583128-G-A		not specified	Uncertain significance (Mar 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPWD1	protein_coding	protein_coding	ENST00000261308	11	24314

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000398	1.00	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.28	291	359	0.810	0.0000182	4311
Missense in Polyphen		72	117.55	0.6125		1422
Synonymous	1.23	99	116	0.855	0.00000571	1182
Loss of Function	3.09	13	31.8	0.409	0.00000207	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000626	0.000608
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000231	0.000229
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: PPIase that catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides and may therefore assist protein folding (PubMed:20676357). May be involved in pre- mRNA splicing (PubMed:11991638). {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:20676357}.
• Pathway: Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.832
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.12

Haploinsufficiency Scores

• pHI: 0.421
• hipred: N
• hipred_score: 0.488
• ghis: 0.667

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.236

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppwd1

Gene ontology

• Biological process: mRNA splicing, via spliceosome;protein peptidyl-prolyl isomerization
• Cellular component: nucleoplasm;nuclear body;catalytic step 2 spliceosome
• Molecular function: peptidyl-prolyl cis-trans isomerase activity;cyclosporin A binding