EID2

protein-coding

EP300 interacting inhibitor of differentiation 2

Gene summary

Enables SMAD binding activity. Involved in several processes, including negative regulation of transcription by RNA polymerase II; negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway; and transforming growth factor beta receptor complex assembly. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CRI2

MANE transcript

NM_153232.4

Inheritance

—

ClinVar variants

U:30B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr19:39,538,707-39,540,161

External References & Databases

Ensembl (ENSG00000176396)

Transcript & Mutation Effects

hg38 • Region Span ~1.5 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 EID2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 31

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153232.4. 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						0
missense			30 clinvar	1 clinvar		31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	1	0	31

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153232.4	RefSeq	NP_694964.3	1	MANE Select
ENST00000390658.4	Ensembl	ENSP00000375073.2	1	MANE Select
ENST00001129570.1	Ensembl	ENSP00000799375.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TGF-beta Signaling Pathway
TGF_beta_Receptor

Biological Process

negative regulation of transcription by RNA polymerase II
transforming growth factor beta receptor complex assembly
SMAD protein complex assembly
muscle organ development
regulation of transforming growth factor beta receptor signaling pathway

Molecular Function

protein binding
SMAD binding

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000390658
Coding exons: 1
Length: 1981
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	0.796	97	122	0.797	0.00000565	1484
Missense (PolyPhen)		2	4.2259	0.47327		41
Synonymous	0.517	49	53.8	0.910	0.00000257	524
Loss of Function	1.37	1	3.94	0.254	1.79e-7	52

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: Interacts with EP300 and acts as a repressor of MYOD- dependent transcription and muscle differentiation. Inhibits EP300 histone acetyltransferase activity. Acts as a repressor of TGFB/SMAD transcriptional responses. May act as a repressor of the TGFB/SMAD3-dependent signaling by selectively blocking formation of TGFB-induced SMAD3-SMAD4 complex. {ECO:0000269|PubMed:12586827, ECO:0000269|PubMed:14585496, ECO:0000269|PubMed:14612439}.;

Recessive Scores

pRec: 0.0973

Intolerance Scores

RVIS EVS: 0.46
RVIS percentile EVS: 78.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.741

Gene Damage Prediction

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