NR2C2AP

nuclear receptor 2C2 associated protein

Basic information

Region (hg38): 19:19201409-19203414

Links

ENSG00000184162 ∙ NCBI:126382 ∙ OMIM:608719 ∙ HGNC:30763 ∙ Uniprot:Q86WQ0 ∙ 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 NR2C2AP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NR2C2AP 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1	9	11	1	22
Total	0	1	20	11	1

Variants in NR2C2AP

This is a list of pathogenic ClinVar variants found in the NR2C2AP region.

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

Position	Type	Phenotype	Significance	ClinVar
19-19201629-T-C		MHC class II deficiency	Likely benign (Oct 10, 2021)
19-19201641-C-G		MHC class II deficiency	Likely benign (Sep 28, 2024)
19-19201642-A-G		MHC class II deficiency	Likely benign (Dec 26, 2024)
19-19201643-T-C		MHC class II deficiency	Likely benign (Sep 01, 2023)
19-19201644-C-A		MHC class II deficiency	Likely benign (Jul 30, 2024)
19-19201648-G-A		MHC class II deficiency	Pathogenic/Likely pathogenic (Mar 17, 2024)
19-19201657-G-T		MHC class II deficiency	Uncertain significance (Dec 02, 2022)
19-19201662-C-G		MHC class II deficiency	Uncertain significance (Feb 03, 2025)
19-19201675-C-T		Inborn genetic diseases	Uncertain significance (Sep 27, 2021)
19-19201677-C-G		MHC class II deficiency	Likely benign (Oct 27, 2023)
19-19201681-C-G		MHC class II deficiency • Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
19-19201687-C-G		MHC class II deficiency	Benign/Likely benign (Feb 02, 2025)
19-19201690-A-G		MHC class II deficiency	Uncertain significance (Jul 06, 2022)
19-19201695-C-T		MHC class II deficiency	Likely benign (Aug 23, 2022)
19-19201698-G-T		MHC class II deficiency	Likely benign (May 08, 2022)
19-19201701-G-A		MHC class II deficiency	Conflicting classifications of pathogenicity (Jan 11, 2025)
19-19201702-C-T		MHC class II deficiency	Uncertain significance (Jun 03, 2022)
19-19201705-G-T		Inborn genetic diseases	Uncertain significance (Sep 27, 2021)
19-19201710-C-G		Inborn genetic diseases	Uncertain significance (Dec 17, 2023)
19-19201711-C-T		MHC class II deficiency	Likely benign (Jan 12, 2025)
19-19201714-G-A		MHC class II deficiency • Inborn genetic diseases	Uncertain significance (Feb 14, 2023)
19-19201728-T-C		MHC class II deficiency • RFXANK-related disorder	Likely benign (Jun 14, 2016)
19-19201731-C-T		MHC class II deficiency	Benign (May 19, 2017)
19-19201936-C-T		not specified	Uncertain significance (Dec 10, 2024)
19-19202335-A-T		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NR2C2AP	protein_coding	protein_coding	ENST00000331552	5	2009

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.244	0.728	125730	0	15	125745	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.239	89	82.9	1.07	0.00000499	906
Missense in Polyphen		32	27.563	1.161		349
Synonymous	0.710	26	31.0	0.838	0.00000166	274
Loss of Function	1.85	2	7.45	0.269	3.18e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a repressor of NR2C2-mediated transactivation by suppressing the binding between NR2C2/TR4 and the TR4-response element in target genes. {ECO:0000269|PubMed:12486131}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;Nuclear Receptor transcription pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0946

Intolerance Scores

• loftool: 0.550
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.337
• hipred: N
• hipred_score: 0.355
• ghis: 0.607

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nr2c2ap

Gene ontology

• Biological process: transcription initiation from RNA polymerase II promoter
• Cellular component: nucleoplasm
• Molecular function: protein binding