AEBP2

protein-coding

AE binding protein 2, the group of Zinc fingers C2H2-type

Gene summary

Predicted to enable DNA binding activity; transcription coregulator activity; and zinc ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within regulation of DNA-templated transcription. Located in nucleoplasm. Part of ESC/E(Z) complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_153207.5

Inheritance

—

ClinVar variants

U:68B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr12:19,404,045-19,720,801

External References & Databases

Ensembl (ENSG00000139154)

Transcript & Mutation Effects

hg38 • Region Span ~316.8 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 AEBP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153207.5. 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						0
missense			66 clinvar	1 clinvar		67
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)						0
Total	0	0	68	1	0	69

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153207.5	RefSeq	NP_694939.2	8	MANE Select
ENST00000266508.14	Ensembl	ENSP00000266508.9	8	MANE Select
NM_001114176.2	RefSeq	NP_001107648.1	9	Standard
NM_001267043.2	RefSeq	NP_001253972.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Histone Modifications
Mesodermal Commitment Pathway
Interactome of polycomb repressive complex 2 (PRC2)
Epigenetic regulation of gene expression
Gene expression (Transcription)

Biological Process

negative regulation of transcription by RNA polymerase II
chromatin organization
negative regulation of gene expression, epigenetic

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription repressor activity, RNA polymerase II-specific
transcription corepressor activity
metal ion binding

Cellular Component

nucleus
nucleoplasm
ESC/E(Z) complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398864
Coding exons: 9
Length: 316757
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.21	135	229	0.589	0.0000117	3361
Missense (PolyPhen)		7	54.217	0.12911		740
Synonymous	-1.19	94	80.4	1.17	0.00000402	956
Loss of Function	4.21	0	20.7	0.00	0.00000129	270

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: DNA-binding transcriptional repressor. May interact with and stimulate the activity of the PRC2 complex, which methylates 'Lys-9' and 'Lys-27' residues of histone H3. {ECO:0000269|PubMed:15225548}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.121
RVIS EVS: -0.01
RVIS percentile EVS: 52.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.993

Gene Damage Prediction

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