NAB1

protein-coding

NGFI-A binding protein 1

Gene summary

Predicted to enable transcription coregulator activity. Predicted to be involved in regulation of DNA-templated transcription. Predicted to act upstream of or within endochondral ossification; nervous system development; and regulation of epidermis development. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_005966.4

Inheritance

—

ClinVar variants

U:56B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr2:190,646,746-190,692,766

External References & Databases

Ensembl (ENSG00000138386)

Transcript & Mutation Effects

hg38 • Region Span ~46.0 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 NAB1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 53

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005966.4. 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				1 clinvar		1
missense			54 clinvar	1 clinvar		55
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	56	2	0	58

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 168 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005966.4	RefSeq	NP_005957.2	7	MANE Select
ENST00000337386.10	Ensembl	ENSP00000336894.5	7	MANE Select
NM_001321312.2	RefSeq	NP_001308241.1	7	Standard
NM_001321313.1	RefSeq	NP_001308242.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endochondral ossification
regulation of transcription, DNA-templated
Schwann cell differentiation
myelination
regulation of epidermis development

Molecular Function

transcription factor binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000337386
Coding exons: 7
Length: 46021
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 16
Defined: 125748
p: 0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.35	194	255	0.762	0.0000125	3173
Missense (PolyPhen)		63	99.155	0.63537		1283
Synonymous	0.453	95	101	0.943	0.00000542	938
Loss of Function	3.00	7	22.3	0.314	0.00000115	279

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.000033	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a transcriptional repressor for zinc finger transcription factors EGR1 and EGR2. {ECO:0000250}.;

Recessive Scores

pRec: 0.134

Intolerance Scores

LoFtool: 0.106
RVIS EVS: -0.49
RVIS percentile EVS: 22.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.848

Gene Damage Prediction

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