EME2

essential meiotic structure-specific endonuclease subunit 2

Basic information

Region (hg38): 16:1772809-1781708

Links

ENSG00000197774 ∙ NCBI:197342 ∙ OMIM:610886 ∙ HGNC:27289 ∙ Uniprot:A4GXA9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EME2 gene.

• not provided (40 variants)
• Inborn genetic diseases (29 variants)
• Combined oxidative phosphorylation deficiency 32 (3 variants)
• Leigh syndrome (1 variants)
• Mitochondrial disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EME2 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				2	1	3
missense					3	3
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		2	47	8	5	62
Total	0	2	47	10	10

Variants in EME2

This is a list of pathogenic ClinVar variants found in the EME2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1772813-C-G			Uncertain significance (Oct 08, 2022)
16-1772829-G-A		MRPS34-related disorder	Likely benign (Jan 12, 2023)
16-1772831-G-A		Mitochondrial disease	Uncertain significance (May 22, 2023)
16-1772837-A-C			Uncertain significance (Oct 30, 2023)
16-1772840-A-G			Uncertain significance (Oct 25, 2021)
16-1772844-C-G			Likely benign (Jul 12, 2023)
16-1772846-G-T			Uncertain significance (Sep 27, 2022)
16-1772860-C-G			Uncertain significance (Jul 17, 2022)
16-1772869-G-A			Uncertain significance (Aug 05, 2022)
16-1772880-G-A			Likely benign (Feb 09, 2022)
16-1772884-A-C		Inborn genetic diseases	Uncertain significance (Oct 05, 2023)
16-1772888-G-A			Uncertain significance (Oct 17, 2022)
16-1772890-C-T			Uncertain significance (Jul 05, 2022)
16-1772932-C-A		Inborn genetic diseases	Uncertain significance (Jun 17, 2022)
16-1772932-C-T		Inborn genetic diseases	Uncertain significance (Jan 15, 2024)
16-1772946-C-G		MRPS34-related disorder	Benign (Jan 30, 2024)
16-1772956-C-A			Uncertain significance (Aug 10, 2023)
16-1772956-C-T			Pathogenic (Nov 22, 2023)
16-1772967-C-T			Likely benign (Oct 13, 2023)
16-1772972-G-A			Likely benign (May 01, 2023)
16-1772974-C-T		Inborn genetic diseases	Uncertain significance (Sep 27, 2021)
16-1772982-A-G			Likely benign (Sep 12, 2023)
16-1772984-A-G		Inborn genetic diseases	Uncertain significance (Mar 07, 2024)
16-1772995-G-A		Inborn genetic diseases	Uncertain significance (Jul 06, 2022)
16-1772999-A-G		MRPS34-related disorder	Benign/Likely benign (Nov 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EME2	protein_coding	protein_coding	ENST00000568449	8	8502

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.76e-23	0.0000113	125462	0	155	125617	0.000617

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.78	309	233	1.33	0.0000150	2328
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00333	0.00332
Ashkenazi Jewish	0.00150	0.00149
East Asian	0.000219	0.000218
Finnish	0.0000964	0.0000924
European (Non-Finnish)	0.000542	0.000528
Middle Eastern	0.000219	0.000218
South Asian	0.000295	0.000294
Other	0.00115	0.00114

dbNSFP

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}.
• Pathway: 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;Homology Directed Repair;Resolution of D-loop Structures through Holliday Junction Intermediates;Resolution of D-Loop Structures;HDR through Homologous Recombination (HRR) (Consensus)

Recessive Scores

• pRec: 0.0956

Haploinsufficiency Scores

• pHI: 0.0879
• hipred: N
• hipred_score: 0.146
• ghis: 0.506

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.547

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Eme2

Gene ontology

• Biological process: resolution of meiotic recombination intermediates;double-strand break repair;replication fork processing;intra-S DNA damage checkpoint;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nuclear chromatin;Holliday junction resolvase complex
• Molecular function: DNA binding;protein binding;crossover junction endodeoxyribonuclease activity