RPAP3

RNA polymerase II associated protein 3, the group of R2TP complex|Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 12:47661249-47706030

Links

ENSG00000005175 ∙ NCBI:79657 ∙ OMIM:611477 ∙ HGNC:26151 ∙ Uniprot:Q9H6T3 ∙ 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 RPAP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPAP3 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			32	3		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	3	0

Variants in RPAP3

This is a list of pathogenic ClinVar variants found in the RPAP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-47663543-T-C		not specified	Uncertain significance (Jan 11, 2023)
12-47667027-T-C		not specified	Likely benign (Oct 12, 2021)
12-47667028-T-C		not specified	Uncertain significance (May 26, 2023)
12-47667037-A-G		not specified	Uncertain significance (Jun 24, 2022)
12-47667815-T-C		not specified	Uncertain significance (May 15, 2023)
12-47668933-A-C		not specified	Uncertain significance (Dec 28, 2023)
12-47668944-G-C		not specified	Uncertain significance (Aug 22, 2023)
12-47668976-C-A		not specified	Uncertain significance (Dec 06, 2022)
12-47669001-G-A		not specified	Uncertain significance (Dec 11, 2023)
12-47669061-C-T		not specified	Uncertain significance (Jan 08, 2024)
12-47669080-C-T		not specified	Uncertain significance (Jun 06, 2023)
12-47670170-G-A		not specified	Uncertain significance (Nov 21, 2022)
12-47670171-T-G		not specified	Uncertain significance (Jan 10, 2023)
12-47670180-G-A		not specified	Uncertain significance (Dec 28, 2022)
12-47670232-A-C		not specified	Uncertain significance (Apr 05, 2023)
12-47670261-G-A		not specified	Uncertain significance (Jan 20, 2023)
12-47670294-T-A		not specified	Uncertain significance (May 24, 2024)
12-47670311-C-T		not specified	Uncertain significance (Sep 23, 2023)
12-47670324-T-G		not specified	Uncertain significance (Feb 17, 2024)
12-47670327-T-A		not specified	Uncertain significance (Aug 18, 2023)
12-47679504-G-A		not specified	Uncertain significance (Jan 03, 2022)
12-47679512-G-A		not specified	Uncertain significance (May 30, 2024)
12-47679527-T-G		not specified	Uncertain significance (Dec 26, 2023)
12-47681778-T-A		not specified	Uncertain significance (Apr 07, 2023)
12-47686844-C-T		not specified	Uncertain significance (Oct 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPAP3	protein_coding	protein_coding	ENST00000005386	16	42775

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000699	1.00	125703	0	41	125744	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.425	303	325	0.934	0.0000157	4370
Missense in Polyphen		124	137.5	0.9018		1961
Synonymous	-0.00702	115	115	1.00	0.00000601	1173
Loss of Function	3.58	14	37.7	0.371	0.00000195	504

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000312	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.000334	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000197	0.000193
Middle Eastern	0.000334	0.000326
South Asian	0.000256	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Forms an interface between the RNA polymerase II enzyme and chaperone/scaffolding protein, suggesting that it is required to connect RNA polymerase II to regulators of protein complex formation. {ECO:0000269|PubMed:17643375}.

Recessive Scores

• pRec: 0.0963

Intolerance Scores

• loftool: 0.922
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.06

Haploinsufficiency Scores

• pHI: 0.427
• hipred: Y
• hipred_score: 0.695
• ghis: 0.662

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.693

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpap3

Gene ontology

• Cellular component: cytosol;R2TP complex
• Molecular function: protein binding