RPAP2

RNA polymerase II associated protein 2

Basic information

Region (hg38): 1:92299059-92402056

Previous symbols: [ "C1orf82" ]

Links

ENSG00000122484 ∙ NCBI:79871 ∙ OMIM:611476 ∙ HGNC:25791 ∙ Uniprot:Q8IXW5 ∙ 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 RPAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPAP2 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			29			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	29	0	0

Variants in RPAP2

This is a list of pathogenic ClinVar variants found in the RPAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-92299077-G-A		not specified	Uncertain significance (Dec 01, 2022)
1-92299111-A-G		not specified	Uncertain significance (Aug 01, 2022)
1-92299126-G-A		not specified	Uncertain significance (May 24, 2023)
1-92301523-G-A		not specified	Uncertain significance (Nov 02, 2023)
1-92301564-A-G		not specified	Uncertain significance (Oct 27, 2021)
1-92301565-T-A		not specified	Uncertain significance (Aug 17, 2022)
1-92304010-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-92304023-G-A		not specified	Uncertain significance (Aug 03, 2022)
1-92304028-A-G		not specified	Uncertain significance (Jun 24, 2022)
1-92304049-C-G		not specified	Uncertain significance (Mar 25, 2024)
1-92307219-C-T		not specified	Uncertain significance (Jan 31, 2024)
1-92323560-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-92323659-A-G		not specified	Uncertain significance (Apr 18, 2023)
1-92323692-T-C		not specified	Uncertain significance (Dec 07, 2023)
1-92323782-T-C		not specified	Uncertain significance (Sep 29, 2022)
1-92323785-G-A		not specified	Uncertain significance (Aug 09, 2021)
1-92323903-G-A		not specified	Uncertain significance (Jun 11, 2021)
1-92323988-G-C		not specified	Uncertain significance (May 15, 2024)
1-92324082-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-92324122-C-T		not specified	Uncertain significance (Apr 28, 2023)
1-92324257-T-C		not specified	Uncertain significance (Jun 28, 2022)
1-92324282-A-C		not specified	Uncertain significance (Nov 09, 2023)
1-92324284-A-T		not specified	Uncertain significance (Nov 21, 2022)
1-92324328-C-T		not specified	Uncertain significance (Dec 27, 2023)
1-92333445-C-T		not specified	Uncertain significance (Sep 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPAP2	protein_coding	protein_coding	ENST00000610020	12	103092

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.58e-7	0.996	125665	0	63	125728	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.735	264	300	0.881	0.0000142	4023
Missense in Polyphen		63	78.913	0.79835		1079
Synonymous	0.680	98	107	0.916	0.00000520	1113
Loss of Function	2.56	16	31.5	0.507	0.00000146	431

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00108	0.00108
Ashkenazi Jewish	0.00	0.00
East Asian	0.000332	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000179	0.000176
Middle Eastern	0.000332	0.000326
South Asian	0.000230	0.000229
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protein phosphatase that displays CTD phosphatase activity and regulates transcription of snRNA genes. Recognizes and binds phosphorylated 'Ser-7' of the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and mediates dephosphorylation of 'Ser-5' of the CTD, thereby promoting transcription of snRNA genes. {ECO:0000269|PubMed:17643375, ECO:0000269|PubMed:22137580, ECO:0000269|PubMed:24997600}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.333
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.0887
• hipred: N
• hipred_score: 0.270
• ghis: 0.616

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.683

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpap2

Gene ontology

• Biological process: snRNA transcription;snRNA transcription by RNA polymerase II;dephosphorylation of RNA polymerase II C-terminal domain
• Cellular component: nucleus;nucleoplasm;nucleolus;cytoplasm;cytosol;RNA polymerase II, holoenzyme
• Molecular function: protein serine/threonine phosphatase activity;protein binding;RNA polymerase II CTD heptapeptide repeat phosphatase activity;RNA polymerase core enzyme binding;metal ion binding