PNRC2

proline rich nuclear receptor coactivator 2

Basic information

Region (hg38): 1:23956839-23963462

Links

ENSG00000189266 ∙ NCBI:55629 ∙ OMIM:611882 ∙ HGNC:23158 ∙ Uniprot:Q9NPJ4 ∙ 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 PNRC2 gene.

• not_specified (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PNRC2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017761.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	9	1	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PNRC2	protein_coding	protein_coding	ENST00000334351	1	4354

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.338	0.497	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.186	10	11.8	0.848	5.40e-7	909
Missense in Polyphen		4	3.5038	1.1416		204
Synonymous	-0.945	7	4.46	1.57	2.25e-7	248
Loss of Function	0.666	0	0.517	0.00	2.22e-8	57

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

• Function: FUNCTION: Involved in nonsense-mediated mRNA decay (NMD) by acting as a bridge between the mRNA decapping complex and the NMD machinery (PubMed:19150429). May act by targeting the NMD machinery to the P-body and recruiting the decapping machinery to aberrant mRNAs (PubMed:19150429). Required for UPF1/RENT1 localization to the P-body (PubMed:19150429). Plays a role in glucocorticoid receptor-mediated mRNA degradation by interacting with the glucocorticoid receptor NR3C1 in a ligand-dependent manner when it is bound to the 5' UTR of target mRNAs and recruiting the RNA helicase UPF1 and the mRNA-decapping enzyme DCP1A, leading to RNA decay (PubMed:25775514). Also acts as a nuclear receptor coactivator (PubMed:11574675). May play a role in controlling the energy balance between energy storage and energy expenditure (By similarity). {ECO:0000250|UniProtKB:Q9CR73, ECO:0000269|PubMed:11574675, ECO:0000269|PubMed:19150429, ECO:0000269|PubMed:25775514}.

Recessive Scores

• pRec: 0.112

Haploinsufficiency Scores

• pHI: 0.621
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pnrc2
• Phenotype: liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;deadenylation-independent decapping of nuclear-transcribed mRNA
• Cellular component: P-body;nucleus;nucleoplasm;Golgi apparatus;cytosol
• Molecular function: protein binding