EME2

protein-coding

essential meiotic structure-specific endonuclease subunit 2

Gene summary

EME2 forms a heterodimer with MUS81 (MIM 606591) that functions as an XPF (MIM 278760)-type flap/fork endonuclease in DNA repair (Ciccia et al., 2007 [PubMed 17289582]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_001257370.2

Inheritance

—

ClinVar variants

P:1U:6B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.61

Max pathogenic AF

—

Genomic locus

chr16:1,772,810-1,781,708

External References & Databases

Ensembl (ENSG00000197774)

Transcript & Mutation Effects

hg38 • Region Span ~8.9 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 EME2 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 8

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001257370.2. 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			2 clinvar	3 clinvar	1 clinvar	6
missense			3 clinvar		3 clinvar	6
nonsense					1 clinvar	1
start loss	1 clinvar					1
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	0	6	3	5	15

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001257370.2	RefSeq	NP_001244299.1	8	MANE Select
ENST00000568449.7	Ensembl	ENSP00000457353.1	8	MANE Select
ENST00000561903.6	Ensembl	ENSP00000457966.2	4	Standard
ENST00000564182.1	Ensembl	ENSP00000456946.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Fanconi anemia pathway - Homo sapiens (human)
HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
Fanconi Anemia Pathway
DNA Repair
DNA Double-Strand Break Repair

Biological Process

resolution of meiotic recombination intermediates
double-strand break repair
replication fork processing
intra-S DNA damage checkpoint
nucleic acid phosphodiester bond hydrolysis

Molecular Function

DNA binding
protein binding
crossover junction endodeoxyribonuclease activity

Cellular Component

nuclear chromatin
Holliday junction resolvase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000568449
Coding exons: 8
Length: 8502
Individuals with no LoFs: 125462
Homozygous LoFs: 0
Heterozygous LoFs: 155
Defined: 125617
p: 0.000617

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.78	309	233	1.33	0.0000150	2328
Missense (PolyPhen)		103	72.393	1.4228		840
Synonymous	-2.90	139	102	1.37	0.00000646	848
Loss of Function	-2.35	28	17.4	1.61	7.61e-7	174

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0031	0.0031	notable
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.0015	0.0015	notable
East Asian	0.00022	0.00022	rare
Finnish	0.000096	0.000092	rare
European (Non-Finnish)	0.00054	0.00053	rare
South Asian	0.00029	0.00029	rare
Other	0.0011	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Interacts with MUS81 to form a DNA structure-specific endonuclease which cleaves substrates such as 3'-flap structures. {ECO:0000269|PubMed:17289582}.;

Recessive Scores

pRec: 0.0956

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.547

Gene Damage Prediction

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