MBIP

protein-coding

MAP3K12 binding inhibitory protein 1, the group of ATAC complex

Gene summary

Enables identical protein binding activity and protein kinase inhibitor activity. Involved in several processes, including positive regulation of JNK cascade; regulation of gene expression; and regulation of tubulin deacetylation. Located in cytosol; nucleolus; and nucleoplasm. Part of ATAC complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_016586.3

Inheritance

—

ClinVar variants

U:38B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr14:36,298,564-36,320,637

External References & Databases

Ensembl (ENSG00000151332)

Transcript & Mutation Effects

hg38 • Region Span ~22.1 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 MBIP variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 38

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016586.3. 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			36 clinvar	3 clinvar		39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	38	3	0	41

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016586.3	RefSeq	NP_057670.2	9	MANE Select
ENST00000416007.9	Ensembl	ENSP00000399718.2	9	MANE Select
NM_001144891.2	RefSeq	NP_001138363.1	9	Standard
NM_001308110.2	RefSeq	NP_001295039.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

EGF-Ncore
Chromatin modifying enzymes
HATs acetylate histones
Chromatin organization

Biological Process

inactivation of MAPK activity involved in osmosensory signaling pathway
molybdopterin cofactor biosynthetic process
histone H3 acetylation

Molecular Function

protein kinase inhibitor activity
protein binding
molybdopterin synthase activity
identical protein binding

Cellular Component

nucleus
Ada2/Gcn5/Ada3 transcription activator complex
nucleolus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000416007
Coding exons: 9
Length: 22113
Individuals with no LoFs: 125687
Homozygous LoFs: 1
Heterozygous LoFs: 60
Defined: 125748
p: 0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.141	170	175	0.970	0.00000837	2251
Missense (PolyPhen)		65	68.338	0.95115		954
Synonymous	-0.0645	64	63.3	1.01	0.00000324	628
Loss of Function	1.90	11	20.2	0.543	0.00000112	234

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00035	0.00035	rare
South Asian	0.00031	0.00026	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inhibits the MAP3K12 activity to induce the activation of the JNK/SAPK pathway. Component of the ATAC complex, a complex with histone acetyltransferase activity on histones H3 and H4. {ECO:0000269|PubMed:19103755}.;

Recessive Scores

pRec: 0.0795

Intolerance Scores

LoFtool: 0.939
RVIS EVS: -0.05
RVIS percentile EVS: 50.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.941

Gene Damage Prediction

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