IER2

protein-coding

immediate early response 2

Gene summary

Predicted to enable DNA binding activity. Involved in cell motility and positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleoplasm. Implicated in colorectal cancer and hepatocellular carcinoma. Biomarker of childhood acute myeloid leukemia; colorectal adenocarcinoma; hepatocellular carcinoma; and melanoma. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_004907.3

Inheritance

—

ClinVar variants

U:36B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr19:13,150,411-13,156,981

External References & Databases

Ensembl (ENSG00000160888)

Transcript & Mutation Effects

hg38 • Region Span ~6.6 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 IER2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004907.3. 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						0
missense			36 clinvar		1 clinvar	37
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	36	0	1	37

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004907.3	RefSeq	NP_004898.2	1	MANE Select
ENST00000292433.4	Ensembl	ENSP00000292433.2	1	MANE Select
ENST00000587885.1	Ensembl	ENSP00000467294.1	1	Standard
ENST00000587885.2	Ensembl	ENSP00000467294.1	1	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ier2a	Danio rerio	Structure: whole organism Quality: decreased length abnormal

Gene / Model

Organism

Observed Phenotype

ier2a

Danio rerio

Structure: whole organism

Quality: decreased length

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

neuron differentiation
positive regulation of transcription by RNA polymerase II
cell motility
response to fibroblast growth factor

Molecular Function

RNA polymerase II regulatory region sequence-specific DNA binding
DNA-binding transcription activator activity, RNA polymerase II-specific
DNA binding

Cellular Component

nucleus
nucleoplasm
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000588173
Coding exons: 1
Length: 4494
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	-0.531	134	118	1.14	0.00000536	1375
Missense (PolyPhen)		43	47.319	0.90872		587
Synonymous	-2.63	79	54.3	1.45	0.00000253	484
Loss of Function	2.04	0	4.83	0.00	2.18e-7	57

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 protein that seems to act as a transcription factor (PubMed:19584537). Involved in the regulation of neuronal differentiation, acts upon JNK-signaling pathway activation and plays a role in neurite outgrowth in hippocampal cells (By similarity). May mediate with FIBP FGF-signaling in the establishment of laterality in the embryo (By similarity). Promotes cell motility, seems to stimulate tumor metastasis (PubMed:22120713). {ECO:0000250|UniProtKB:B7SXM5, ECO:0000250|UniProtKB:Q6P7D3, ECO:0000269|PubMed:19584537, ECO:0000269|PubMed:22120713}.;

Recessive Scores

pRec: 0.131

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.984

Gene Damage Prediction

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