PRRC2A

protein-coding

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

Gene summary

A cluster of genes, BAT1-BAT5, has been localized in the vicinity of the genes for TNF alpha and TNF beta. These genes are all within the human major histocompatibility complex class III region. This gene has microsatellite repeats which are associated with the age-at-onset of insulin-dependent diabetes mellitus (IDDM) and possibly thought to be involved with the inflammatory process of pancreatic beta-cell destruction during the development of IDDM. This gene is also a candidate gene for the development of rheumatoid arthritis. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2010]

Previous symbols:

BAT2

MANE transcript

NM_004638.4

Inheritance

—

ClinVar variants

U:406B:57

Top phenotype

PRRC2A-related disorder

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr6:31,620,715-31,637,771

External References & Databases

Ensembl (ENSG00000204469)

Transcript & Mutation Effects

hg38 • Region Span ~17.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRRC2A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 384

PRRC2A-related disorderTotal: 51

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004638.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	18 clinvar	6 clinvar	29
missense			386 clinvar	18 clinvar	15 clinvar	419
nonsense			3 clinvar			3
start loss						0
frameshift			4 clinvar			4
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	0	406	36	21	463

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004638.4	RefSeq	NP_004629.3	30	MANE Select
ENST00000376033.3	Ensembl	ENSP00000365201.2	30	MANE Select
NM_080686.3	RefSeq	NP_542417.2	30	Standard
ENST00000376007.8	Ensembl	ENSP00000365175.4	30	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding
protein binding

Cellular Component

nucleoplasm
cytosol
plasma membrane
membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376033
Coding exons: 30
Length: 17052
Individuals with no LoFs: 125689
Homozygous LoFs: 0
Heterozygous LoFs: 59
Defined: 125748
p: 0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.184	1323	1.30e+3	1.01	0.0000845	13500
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000069	0.000062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0017	0.0017	notable
Finnish	0.000094	0.000092	rare
European (Non-Finnish)	0.00015	0.00014	rare
South Asian	0.00013	0.00013	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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