IER3IP1

immediate early response 3 interacting protein 1

Basic information

Region (hg38): 18:47152834-47176364

Links

ENSG00000134049 ∙ NCBI:51124 ∙ OMIM:609382 ∙ HGNC:18550 ∙ Uniprot:Q9Y5U9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• primary microcephaly-epilepsy-permanent neonatal diabetes syndrome (Strong), mode of inheritance: AR
• primary microcephaly-epilepsy-permanent neonatal diabetes syndrome (Supportive), mode of inheritance: AR
• microcephaly, epilepsy, and diabetes syndrome 1 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Microcephaly, epilepsy, and diabetes syndrome 1	AR	Endocrine	Among other findings, individuals may have early-onset diabetes, which may be difficult to control, and awareness may allow early diagnosis and medical management	Endocrine; Neurologic	16972080; 21835305; 24138066
Individuals may have early-onset diabetes, which may be difficult to control

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IER3IP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IER3IP1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				30		30
missense		1	34			35
nonsense			2			2
start loss			2			2
frameshift			3			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	5		6
non coding			2	13	10	25
Total	0	1	43	43	10

Variants in IER3IP1

This is a list of pathogenic ClinVar variants found in the IER3IP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
18-47156119-A-G		Childhood epilepsy with centrotemporal spikes • IER3IP1-related disorder • Epilepsy	Conflicting classifications of pathogenicity (May 24, 2021)
18-47156178-C-T		Microcephaly, epilepsy, and diabetes syndrome	Likely benign (Feb 26, 2021)
18-47156187-A-C		Microcephaly, epilepsy, and diabetes syndrome	Uncertain significance (Jun 26, 2019)
18-47156188-A-G		Microcephaly, epilepsy, and diabetes syndrome	Likely benign (Dec 07, 2023)
18-47156192-A-G		Microcephaly, epilepsy, and diabetes syndrome	Likely benign (Aug 27, 2023)
18-47156193-A-G		Microcephaly, epilepsy, and diabetes syndrome • Microcephaly, epilepsy, and diabetes syndrome 1	Pathogenic/Likely pathogenic (May 07, 2022)
18-47156195-T-C		Microcephaly, epilepsy, and diabetes syndrome	Likely benign (Sep 27, 2022)
18-47156196-A-T		Microcephaly, epilepsy, and diabetes syndrome	Uncertain significance (Jun 25, 2021)
18-47156200-C-A		Microcephaly, epilepsy, and diabetes syndrome	Uncertain significance (Oct 13, 2023)
18-47156203-T-C		Microcephaly, epilepsy, and diabetes syndrome	Uncertain significance (Aug 23, 2022)
18-47156205-G-C		Microcephaly, epilepsy, and diabetes syndrome	Uncertain significance (Aug 16, 2022)
18-47156208-A-G		Microcephaly, epilepsy, and diabetes syndrome	Uncertain significance (Jun 18, 2022)
18-47156209-T-C		Microcephaly, epilepsy, and diabetes syndrome	Uncertain significance (Jul 19, 2022)
18-47156211-G-A		Microcephaly, epilepsy, and diabetes syndrome	Uncertain significance (Sep 19, 2022)
18-47156226-A-G		Microcephaly, epilepsy, and diabetes syndrome	Uncertain significance (Feb 07, 2022)
18-47156227-A-G		Microcephaly, epilepsy, and diabetes syndrome	Likely benign (Mar 14, 2023)
18-47156235-G-A		Microcephaly, epilepsy, and diabetes syndrome	Uncertain significance (Aug 27, 2021)
18-47156242-G-A			Likely benign (Sep 19, 2017)
18-47156242-GA-G		Microcephaly, epilepsy, and diabetes syndrome	Benign (Oct 04, 2023)
18-47156242-GAAAA-G		Microcephaly, epilepsy, and diabetes syndrome	Likely benign (Dec 07, 2023)
18-47156242-G-GA		Microcephaly, epilepsy, and diabetes syndrome	Benign (Jun 05, 2023)
18-47156244-A-G		Microcephaly, epilepsy, and diabetes syndrome	Likely benign (Apr 18, 2022)
18-47156489-G-C			Likely benign (Mar 17, 2019)
18-47156520-C-T			Benign (Jun 16, 2018)
18-47156522-G-T			Benign (Jun 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IER3IP1	protein_coding	protein_coding	ENST00000256433	3	21333

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0234	0.784	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.392	50	42.8	1.17	0.00000212	504
Missense in Polyphen		11	14.839	0.74127		181
Synonymous	-1.23	25	18.3	1.37	9.92e-7	175
Loss of Function	0.953	3	5.39	0.557	2.95e-7	51

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000164	0.000155
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be implicated in the regulation of apoptosis. May be involved in protein transport between endoplasmic reticulum and Golgi apparatus (By similarity). {ECO:0000250}.

Intolerance Scores

• loftool: 0.516
• rvis_EVS: 0.26
• rvis_percentile_EVS: 69.83

Haploinsufficiency Scores

• pHI: 0.308
• hipred: N
• hipred_score: 0.146
• ghis: 0.511

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ier3ip1

Zebrafish Information Network

• Gene name: ier3ip1
• Affected structure: blood cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;regulation of fibroblast apoptotic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;membrane;COPII-coated ER to Golgi transport vesicle;integral component of Golgi membrane