RPRD1A

regulation of nuclear pre-mRNA domain containing 1A

Basic information

Region (hg38): 18:35984387-36067576

Links

ENSG00000141425 ∙ NCBI:55197 ∙ OMIM:610347 ∙ HGNC:25560 ∙ Uniprot:Q96P16 ∙ 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 RPRD1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPRD1A 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in RPRD1A

This is a list of pathogenic ClinVar variants found in the RPRD1A region.

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

Position	Type	Phenotype	Significance	ClinVar
18-35993188-T-C		not specified	Uncertain significance (Apr 13, 2022)
18-35993290-C-T		not specified	Uncertain significance (Jan 31, 2024)
18-36026910-T-C		not specified	Uncertain significance (Apr 24, 2024)
18-36026937-T-C		not specified	Uncertain significance (Mar 28, 2024)
18-36027033-G-T		not specified	Uncertain significance (Nov 11, 2024)
18-36027283-C-A		not specified	Uncertain significance (Mar 07, 2024)
18-36030845-T-C		not specified	Uncertain significance (Jan 03, 2022)
18-36030896-T-C		not specified	Uncertain significance (May 24, 2024)
18-36033709-T-C		not specified	Uncertain significance (Oct 13, 2023)
18-36067260-G-A		not specified	Uncertain significance (Sep 17, 2021)
18-36067385-G-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPRD1A	protein_coding	protein_coding	ENST00000399022	7	83190

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.222	0.777	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	92	161	0.570	0.00000814	2029
Missense in Polyphen		8	34.852	0.22954		489
Synonymous	-0.374	65	61.3	1.06	0.00000299	588
Loss of Function	2.76	4	15.8	0.253	8.00e-7	203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000137	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts with phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit POLR2A, and participates in dephosphorylation of the CTD by RPAP2. May act as a negative regulator of cyclin-D1 (CCND1) and cyclin-E (CCNE1) in the cell cycle. {ECO:0000269|PubMed:22231121, ECO:0000269|PubMed:24399136, ECO:0000269|PubMed:24997600}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.673
• ghis: 0.713

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.345

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Rprd1a

Gene ontology

• Biological process: mRNA 3'-end processing;snRNA transcription by RNA polymerase II;dephosphorylation of RNA polymerase II C-terminal domain
• Cellular component: nucleoplasm;RNA polymerase II, holoenzyme
• Molecular function: RNA polymerase II complex binding;protein binding