NAB2

NGFI-A binding protein 2

Basic information

Region (hg38): 12:57089043-57095476

Links

ENSG00000166886 ∙ NCBI:4665 ∙ OMIM:602381 ∙ HGNC:7627 ∙ Uniprot:Q15742 ∙ 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 NAB2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAB2 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				1		1
missense			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	1

Variants in NAB2

This is a list of pathogenic ClinVar variants found in the NAB2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-57089335-A-C		not specified	Uncertain significance (Jun 17, 2024)
12-57091127-C-G		not specified	Uncertain significance (Feb 02, 2024)
12-57091136-G-A		not specified	Uncertain significance (May 23, 2023)
12-57091245-C-T			Likely benign (Jan 01, 2023)
12-57091246-G-A		not specified	Uncertain significance (Apr 23, 2024)
12-57091354-G-C		not specified	Uncertain significance (Nov 10, 2022)
12-57091477-G-A		not specified	Uncertain significance (Dec 28, 2023)
12-57091486-G-C		not specified	Uncertain significance (Aug 23, 2021)
12-57091502-G-A		not specified	Uncertain significance (Jan 05, 2022)
12-57091511-G-C		not specified	Uncertain significance (Dec 13, 2022)
12-57091631-C-T		not specified	Uncertain significance (Feb 06, 2023)
12-57091658-C-G		not specified	Uncertain significance (Sep 26, 2024)
12-57091661-C-T		not specified	Uncertain significance (Oct 12, 2021)
12-57091672-C-T			Benign (Jul 21, 2018)
12-57091718-C-G		not specified	Uncertain significance (Jul 30, 2023)
12-57091738-G-T		not specified	Uncertain significance (Aug 15, 2024)
12-57091769-G-A		not specified	Uncertain significance (Sep 12, 2023)
12-57091801-C-T		not specified	Uncertain significance (Nov 15, 2023)
12-57092578-C-A		not specified	Uncertain significance (Aug 13, 2021)
12-57092955-A-G		not specified	Uncertain significance (Feb 12, 2024)
12-57093080-C-A		not specified	Uncertain significance (Jul 26, 2024)
12-57093118-A-G		not specified	Uncertain significance (Dec 13, 2023)
12-57093187-A-C		not specified	Uncertain significance (Aug 31, 2022)
12-57093514-G-A		not specified	Uncertain significance (Mar 07, 2024)
12-57093524-G-A		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAB2	protein_coding	protein_coding	ENST00000300131	7	6583

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.567	0.433	125737	0	3	125740	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.01	168	319	0.526	0.0000197	3315
Missense in Polyphen		36	114.52	0.31436		1159
Synonymous	-1.94	162	133	1.21	0.00000787	1145
Loss of Function	3.30	4	19.9	0.201	0.00000118	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000120	0.0000993
East Asian	0.0000544	0.0000544
Finnish	0.0000544	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a transcriptional repressor for zinc finger transcription factors EGR1 and EGR2. Isoform 2 lacks repression ability (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.165

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.734
• hipred: Y
• hipred_score: 0.775
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nab2
• Phenotype: normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; growth/size/body region 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); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: endochondral ossification;regulation of transcription, DNA-templated;nervous system development;cell population proliferation;Schwann cell differentiation;negative regulation of transcription by RNA polymerase III;myelination;regulation of epidermis development;positive regulation of tau-protein kinase activity
• Cellular component: nucleus
• Molecular function: transcription corepressor activity;protein binding;transcription factor binding;identical protein binding