PAAF1

proteasomal ATPase associated factor 1, the group of WD repeat domain containing

Basic information

Region (hg38): 11:73876699-73931114

Previous symbols: [ "WDR71" ]

Links

ENSG00000175575 ∙ NCBI:80227 ∙ OMIM:619772 ∙ HGNC:25687 ∙ Uniprot:Q9BRP4 ∙ 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 PAAF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PAAF1 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				1		1
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	0

Variants in PAAF1

This is a list of pathogenic ClinVar variants found in the PAAF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-73877061-G-T		not specified	Uncertain significance (Apr 09, 2024)
11-73887356-A-G		not specified	Uncertain significance (Sep 17, 2021)
11-73887392-A-G		not specified	Uncertain significance (Dec 14, 2023)
11-73891140-A-G		not specified	Uncertain significance (Mar 31, 2023)
11-73891195-A-G			Likely benign (Jul 01, 2022)
11-73899213-A-G		not specified	Uncertain significance (Apr 25, 2023)
11-73900330-G-T		not specified	Uncertain significance (Feb 22, 2023)
11-73900359-G-C		not specified	Uncertain significance (Sep 30, 2024)
11-73900369-T-C		not specified	Uncertain significance (Nov 13, 2024)
11-73900393-G-A		not specified	Uncertain significance (Apr 17, 2024)
11-73900409-G-A		not specified	Uncertain significance (Dec 06, 2023)
11-73909419-G-A		not specified	Uncertain significance (Dec 11, 2023)
11-73909434-A-T		not specified	Uncertain significance (Feb 15, 2023)
11-73909468-G-A		not specified	Uncertain significance (Nov 07, 2023)
11-73909486-G-A		not specified	Uncertain significance (Feb 27, 2023)
11-73909486-G-C		not specified	Uncertain significance (Sep 26, 2022)
11-73914481-T-G		not specified	Uncertain significance (Apr 06, 2024)
11-73914496-A-G		not specified	Uncertain significance (Aug 12, 2024)
11-73916569-G-A		not specified	Uncertain significance (Jun 27, 2022)
11-73918955-C-T		not specified	Uncertain significance (Feb 09, 2025)
11-73918961-A-G		not specified	Uncertain significance (Feb 05, 2024)
11-73918984-C-T		not specified	Uncertain significance (Mar 08, 2025)
11-73918994-C-A		not specified	Uncertain significance (Nov 18, 2023)
11-73924645-A-T		not specified	Uncertain significance (May 06, 2022)
11-73927297-G-C		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PAAF1	protein_coding	protein_coding	ENST00000310571	12	51047

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.04e-11	0.226	125424	3	321	125748	0.00129

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.925	176	214	0.822	0.0000109	2535
Missense in Polyphen		51	60.197	0.84722		651
Synonymous	0.690	71	78.8	0.901	0.00000402	773
Loss of Function	0.787	18	22.0	0.819	0.00000110	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000828	0.000822
Ashkenazi Jewish	0.00	0.00
East Asian	0.000707	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000707	0.000653
South Asian	0.00917	0.00859
Other	0.000988	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits proteasome 26S assembly and proteolytic activity by impairing the association of the 19S regulatory complex with the 20S core. In case of HIV-1 infection, recruited by viral Tat to the HIV-1 promoter, where it promotes the recruitment of 19S regulatory complex through dissociation of the proteasome 26S. This presumably promotes provirus transcription efficiency. Protects SUPT6H from proteasomal degradation. {ECO:0000269|PubMed:15831487, ECO:0000269|PubMed:17289585, ECO:0000269|PubMed:22316138}.

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.814
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.250
• hipred: Y
• hipred_score: 0.662
• ghis: 0.504

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0192

Gene Damage Prediction

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

Gene ontology

• Biological process: viral process
• Cellular component: proteasome complex
• Molecular function: protein binding