EPM2AIP1

protein-coding

EPM2A interacting protein 1

Gene summary

The EPM2A gene, which encodes laforin, is mutated in an autosomal recessive form of adolescent progressive myoclonus epilepsy. The protein encoded by this gene binds to laforin, but its function is not known. This gene is intronless. [provided by RefSeq, Oct 2008]

MANE transcript

NM_014805.4

Inheritance

—

ClinVar variants

U:66B:6

Top phenotype

Hereditary nonpolyposis colorectal neoplasms

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr3:36,985,043-36,993,131

External References & Databases

Ensembl (ENSG00000178567)

Transcript & Mutation Effects

hg38 • Region Span ~8.1 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 EPM2AIP1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 68

not providedTotal: 3

Hereditary nonpolyposis colorectal neoplasmsTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014805.4. 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				1 clinvar	2 clinvar	3
missense			66 clinvar	3 clinvar		69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	66	4	2	72

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014805.4	RefSeq	NP_055620.1	1	MANE Select
ENST00000322716.8	Ensembl	ENSP00000406027.1	1	MANE Select
ENST00000623924.1	Ensembl	ENSP00000485489.1	3	Standard
ENST00000624586.1	Ensembl	ENSP00000485091.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

response to insulin
positive regulation of glycogen biosynthetic process
positive regulation of glycogen (starch) synthase activity

Molecular Function

protein binding
identical protein binding

Cellular Component

nucleus
endoplasmic reticulum

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000322716
Coding exons: 1
Length: 7439
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	1.44	251	324	0.774	0.0000153	3984
Missense (PolyPhen)		68	108.06	0.62929		1408
Synonymous	-1.60	149	126	1.18	0.00000616	1204
Loss of Function	3.35	4	20.3	0.197	0.00000118	242

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

Intolerance Scores

LoFtool: 0.526
RVIS EVS: -0.01
RVIS percentile EVS: 53.51

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.914

Gene Damage Prediction

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