NACC2

NACC family member 2, the group of BTB domain containing|BEN domain containing

Basic information

Region (hg38): 9:136006537-136095289

Previous symbols: [ "BTBD14A" ]

Links

ENSG00000148411 ∙ NCBI:138151 ∙ OMIM:615786 ∙ HGNC:23846 ∙ Uniprot:Q96BF6 ∙ 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 NACC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NACC2 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					2	2
missense			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	2

Variants in NACC2

This is a list of pathogenic ClinVar variants found in the NACC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136011538-C-T		not specified	Uncertain significance (Oct 27, 2022)
9-136011562-G-A		not specified	Uncertain significance (Sep 16, 2021)
9-136011587-C-T		not specified	Likely benign (Jul 05, 2024)
9-136011644-C-T		not specified	Uncertain significance (Aug 12, 2024)
9-136011659-C-T		not specified	Uncertain significance (Oct 12, 2021)
9-136011670-G-A		not specified	Uncertain significance (Jan 29, 2024)
9-136011695-C-T		not specified	Uncertain significance (Sep 09, 2024)
9-136011698-C-T		not specified	Uncertain significance (Oct 25, 2022)
9-136011716-C-T		not specified	Likely benign (Nov 21, 2023)
9-136011728-G-C		not specified	Uncertain significance (Dec 18, 2023)
9-136011740-C-T		not specified	Uncertain significance (Jun 25, 2024)
9-136011761-C-T		not specified	Uncertain significance (Aug 02, 2021)
9-136011775-T-G		not specified	Uncertain significance (Jul 14, 2021)
9-136011776-C-T		not specified	Uncertain significance (Oct 17, 2024)
9-136011806-C-T		not specified	Uncertain significance (Aug 04, 2023)
9-136011827-G-C		not specified	Uncertain significance (Apr 07, 2023)
9-136011842-C-T		not specified	Uncertain significance (Mar 22, 2023)
9-136011857-C-T		not specified	Uncertain significance (Jul 20, 2021)
9-136011860-C-T		not specified	Uncertain significance (Jun 07, 2023)
9-136011863-C-A		not specified	Likely benign (Apr 07, 2023)
9-136011872-T-C		not specified	Uncertain significance (Dec 18, 2023)
9-136011872-T-G		not specified	Uncertain significance (Nov 10, 2024)
9-136011875-C-G		not specified	Uncertain significance (Jul 05, 2023)
9-136011893-C-T		not specified	Uncertain significance (Jun 25, 2024)
9-136013208-C-T		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NACC2	protein_coding	protein_coding	ENST00000371753	5	88749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.315	0.670	124834	0	3	124837	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.73	120	186	0.644	0.0000141	3762
Missense in Polyphen		40	82.673	0.48384		1366
Synonymous	-1.42	99	82.6	1.20	0.00000661	1242
Loss of Function	2.04	2	8.35	0.239	3.55e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000122
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: Functions as a transcriptional repressor through its association with the NuRD complex. Recruits the NuRD complex to the promoter of MDM2, leading to the repression of MDM2 transcription and subsequent stability of p53/TP53. {ECO:0000269|PubMed:22926524}.

Haploinsufficiency Scores

• pHI: 0.284
• hipred: Y
• hipred_score: 0.546
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.209

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nacc2
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;positive regulation of cell population proliferation;negative regulation of cell population proliferation;histone deacetylation;cellular protein-containing complex localization;negative regulation of transcription, DNA-templated;protein homooligomerization;negative regulation of G1/S transition of mitotic cell cycle by negative regulation of transcription from RNA polymerase II promoter;positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage
• Cellular component: nuclear chromatin;nucleus;nucleolus;mitochondrion;nuclear body
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;transcription corepressor activity;histone deacetylase activity;protein binding;protein homodimerization activity;histone deacetylase binding;protein-containing complex binding