PRRC2A

proline rich coiled-coil 2A, the group of Small nucleolar RNA protein coding host genes|MicroRNA protein coding host genes

Basic information

Region (hg38): 6:31620714-31637771

Previous symbols: [ "BAT2" ]

Links

ENSG00000204469 ∙ NCBI:7916 ∙ OMIM:142580 ∙ HGNC:13918 ∙ Uniprot:P48634 ∙ 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 PRRC2A gene.

• Inborn genetic diseases (118 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRRC2A 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		3
missense			112	6	1	119
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	113	9	1

Variants in PRRC2A

This is a list of pathogenic ClinVar variants found in the PRRC2A region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31622898-G-A		not specified	Uncertain significance (Jul 14, 2021)
6-31623829-A-G		PRRC2A-related disorder	Likely benign (Mar 12, 2019)
6-31623841-C-T		PRRC2A-related disorder	Likely benign (Feb 19, 2019)
6-31624284-C-T		not specified	Uncertain significance (Oct 27, 2023)
6-31624287-C-T		PRRC2A-related disorder	Benign (Apr 08, 2019)
6-31624305-C-A		not specified	Uncertain significance (Jun 27, 2022)
6-31624444-C-A		PRRC2A-related disorder	Likely benign (May 23, 2019)
6-31624474-G-A		not specified	Uncertain significance (Sep 23, 2023)
6-31624492-G-A		not specified	Uncertain significance (Sep 20, 2023)
6-31625195-C-T		PRRC2A-related disorder	Benign (Feb 19, 2019)
6-31625248-A-G		not specified	Uncertain significance (Nov 10, 2022)
6-31625252-C-G		not specified	Uncertain significance (Jan 09, 2023)
6-31625254-G-T		not specified	Uncertain significance (Jun 29, 2022)
6-31625282-C-T		not specified	Uncertain significance (Jun 05, 2023)
6-31625306-G-A		not specified	Uncertain significance (Feb 24, 2022)
6-31625460-A-T		not specified	Uncertain significance (Mar 03, 2022)
6-31625488-G-T		PRRC2A-related disorder	Benign (Feb 27, 2019)
6-31625489-C-T		not specified	Uncertain significance (Oct 03, 2023)
6-31625522-A-C		not specified	Uncertain significance (Dec 19, 2022)
6-31625543-C-T		not specified	Uncertain significance (Jun 26, 2023)
6-31625544-C-T		not specified	Uncertain significance (Feb 10, 2023)
6-31625782-C-G		PRRC2A-related disorder	Likely benign (Jun 05, 2019)
6-31625805-A-G		not specified	Uncertain significance (Sep 14, 2022)
6-31625814-T-G		not specified	Uncertain significance (Dec 11, 2023)
6-31626021-C-T		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PRRC2A	protein_coding	protein_coding	ENST00000376033	30	17052

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.43e-9	125689	0	59	125748	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.184	1323	1.30e+3	1.01	0.0000845	13500
Missense in Polyphen		7	12.854	0.54458		120
Synonymous	-0.438	514	502	1.02	0.0000295	4894
Loss of Function	8.62	13	111	0.117	0.00000799	1026

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000179
Ashkenazi Jewish	0.00	0.00
East Asian	0.00170	0.00169
Finnish	0.0000942	0.0000924
European (Non-Finnish)	0.000152	0.000141
Middle Eastern	0.00170	0.00169
South Asian	0.000134	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the regulation of pre-mRNA splicing. {ECO:0000269|PubMed:14667819}.

Recessive Scores

• pRec: 0.0960

Intolerance Scores

• rvis_EVS: 2.16
• rvis_percentile_EVS: 98.02

Haploinsufficiency Scores

• pHI: 0.557
• hipred: N
• hipred_score: 0.372
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Prrc2a

Gene ontology

• Cellular component: nucleoplasm;cytosol;plasma membrane;membrane;extracellular exosome
• Molecular function: RNA binding;protein binding