RPAP1

RNA polymerase II associated protein 1

Basic information

Region (hg38): 15:41517176-41544269

Links

ENSG00000103932 ∙ NCBI:26015 ∙ OMIM:611475 ∙ HGNC:24567 ∙ Uniprot:Q9BWH6 ∙ 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 RPAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPAP1 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			115	10	1	126
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	115	10	1

Variants in RPAP1

This is a list of pathogenic ClinVar variants found in the RPAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-41517604-G-A		not specified	Uncertain significance (Sep 27, 2024)
15-41517613-G-T		not specified	Uncertain significance (Nov 21, 2022)
15-41517666-T-C		not specified	Uncertain significance (Aug 04, 2023)
15-41517684-C-T		not specified	Uncertain significance (Aug 27, 2024)
15-41517838-C-T		not specified	Uncertain significance (Dec 04, 2024)
15-41518049-G-A		not specified	Uncertain significance (Feb 05, 2024)
15-41518082-C-T		not specified	Likely benign (Dec 28, 2023)
15-41518089-G-A		not specified	Likely benign (Aug 19, 2024)
15-41518094-G-A		not specified	Uncertain significance (Jul 09, 2021)
15-41520437-C-G		not specified	Uncertain significance (Feb 19, 2025)
15-41520464-C-G		not specified	Uncertain significance (Mar 29, 2024)
15-41520473-C-T		not specified	Uncertain significance (Jan 24, 2025)
15-41520554-T-G		not specified	Uncertain significance (Apr 04, 2024)
15-41520564-G-A		not specified	Uncertain significance (Jul 09, 2024)
15-41520569-G-C		not specified	Uncertain significance (Nov 27, 2024)
15-41520572-G-A		not specified	Uncertain significance (Apr 09, 2024)
15-41520573-T-A		not specified	Uncertain significance (Nov 11, 2024)
15-41520636-C-T		not specified	Uncertain significance (Jan 26, 2023)
15-41520660-G-C		not specified	Uncertain significance (Jul 12, 2023)
15-41520684-C-T		not specified	Uncertain significance (Aug 22, 2023)
15-41520705-A-C		not specified	Uncertain significance (Feb 08, 2025)
15-41520723-G-A		not specified	Uncertain significance (Dec 22, 2023)
15-41520731-G-C		not specified	Uncertain significance (Jun 30, 2024)
15-41520738-C-G		not specified	Uncertain significance (Sep 21, 2021)
15-41520759-G-A		not specified	Uncertain significance (Dec 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPAP1	protein_coding	protein_coding	ENST00000304330	24	27094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.38e-17	0.999	125605	0	143	125748	0.000569

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	681	804	0.847	0.0000473	8786
Missense in Polyphen		175	246.34	0.71039		2755
Synonymous	0.0185	341	341	0.999	0.0000192	3098
Loss of Function	3.13	38	65.3	0.582	0.00000364	675

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00139	0.00138
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000441	0.000435
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000692	0.000686
Middle Eastern	0.000441	0.000435
South Asian	0.000590	0.000588
Other	0.000163	0.000163

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. Required for interaction of the RNA polymerase II complex with acetylated histone H3. {ECO:0000269|PubMed:17643375}.

Recessive Scores

• pRec: 0.0997

Intolerance Scores

• loftool: 0.730
• rvis_EVS: 1.17
• rvis_percentile_EVS: 92.7

Haploinsufficiency Scores

• pHI: 0.0710
• hipred: N
• hipred_score: 0.332
• ghis: 0.484

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.327

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rpap1

Gene ontology

• Biological process: transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA binding;DNA-directed 5'-3' RNA polymerase activity;protein binding