RPRD2

regulation of nuclear pre-mRNA domain containing 2

Basic information

Region (hg38): 1:150363091-150476566

Previous symbols: [ "KIAA0460" ]

Links

ENSG00000163125 ∙ NCBI:23248 ∙ OMIM:614695 ∙ HGNC:29039 ∙ Uniprot:Q5VT52 ∙ 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 RPRD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPRD2 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				3	1	4
missense			53	2		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	5	1

Variants in RPRD2

This is a list of pathogenic ClinVar variants found in the RPRD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-150364751-T-G		not specified	Uncertain significance (Feb 05, 2024)
1-150364779-C-T		not specified	Uncertain significance (Nov 16, 2021)
1-150364893-A-G		not specified	Uncertain significance (Mar 22, 2023)
1-150444268-A-G			Benign (May 14, 2018)
1-150444287-C-T		not specified	Uncertain significance (Dec 06, 2023)
1-150446270-A-C		not specified	Uncertain significance (Nov 16, 2021)
1-150446303-G-C		not specified	Uncertain significance (Aug 22, 2023)
1-150446328-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-150460102-C-A		not specified	Uncertain significance (Jan 26, 2023)
1-150460125-A-G		not specified	Uncertain significance (Oct 12, 2021)
1-150460152-T-C		not specified	Uncertain significance (Oct 20, 2023)
1-150460153-G-A		not specified	Uncertain significance (Oct 12, 2022)
1-150460182-A-G		not specified	Uncertain significance (Mar 19, 2024)
1-150464611-C-T		not specified	Uncertain significance (Sep 29, 2023)
1-150464619-A-C		not specified	Uncertain significance (Jun 16, 2023)
1-150464632-C-T		not specified	Uncertain significance (May 14, 2024)
1-150464649-T-C		not specified	Uncertain significance (May 17, 2023)
1-150470642-C-G		not specified	Uncertain significance (Aug 08, 2022)
1-150471077-G-A		not specified	Uncertain significance (Feb 03, 2022)
1-150471097-A-G		not specified	Likely benign (Nov 15, 2023)
1-150471124-C-T		not specified	Uncertain significance (Jan 11, 2023)
1-150471125-G-A		not specified	Uncertain significance (Oct 29, 2021)
1-150471134-G-A		not specified	Uncertain significance (Jan 16, 2024)
1-150471199-T-C		not specified	Uncertain significance (Jun 09, 2022)
1-150471231-C-T			Likely benign (Apr 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPRD2	protein_coding	protein_coding	ENST00000369068	11	113476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.26e-8	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	623	791	0.788	0.0000418	9445
Missense in Polyphen		195	312.52	0.62397		3810
Synonymous	0.373	296	304	0.973	0.0000159	3108
Loss of Function	6.31	0	46.4	0.00	0.00000260	598

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.53

Haploinsufficiency Scores

• pHI: 0.164
• hipred: Y
• hipred_score: 0.643
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.362

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rprd2

Gene ontology

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