EME1

essential meiotic structure-specific endonuclease 1

Basic information

Region (hg38): 17:50373220-50381483

Links

ENSG00000154920 ∙ NCBI:146956 ∙ OMIM:610885 ∙ HGNC:24965 ∙ Uniprot:Q96AY2 ∙ 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 EME1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EME1 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						0
missense			33	4	1	38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	33	4	1

Variants in EME1

This is a list of pathogenic ClinVar variants found in the EME1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-50375223-G-T			Benign (Oct 10, 2018)
17-50375279-C-G		not specified	Uncertain significance (May 04, 2023)
17-50375327-G-A		not specified	Uncertain significance (Jun 14, 2022)
17-50375332-G-A		not specified	Uncertain significance (Sep 27, 2021)
17-50375339-T-C		not specified	Uncertain significance (Oct 08, 2024)
17-50375404-C-G		not specified	Uncertain significance (Jun 25, 2024)
17-50375405-C-T		not specified	Uncertain significance (Jul 14, 2024)
17-50375410-C-G		not specified	Uncertain significance (Dec 16, 2023)
17-50375476-G-A		not specified	Uncertain significance (Apr 05, 2023)
17-50375525-C-A		not specified	Uncertain significance (Oct 01, 2024)
17-50375532-G-C		not specified	Uncertain significance (Mar 20, 2024)
17-50375539-A-C		not specified	Uncertain significance (Oct 06, 2021)
17-50375588-A-G		not specified	Uncertain significance (Aug 09, 2021)
17-50375659-C-T		not specified	Likely benign (Mar 20, 2023)
17-50375665-A-G		not specified	Uncertain significance (Feb 27, 2024)
17-50375732-C-T		not specified	Uncertain significance (Oct 26, 2021)
17-50375753-G-A		not specified	Uncertain significance (Oct 12, 2024)
17-50375810-C-T		not specified	Uncertain significance (Apr 08, 2024)
17-50375912-C-T		not specified	Uncertain significance (Oct 10, 2023)
17-50375962-A-G		not specified	Likely benign (Jun 21, 2023)
17-50375974-C-G		not specified	Uncertain significance (Oct 29, 2021)
17-50376135-T-C		not specified	Uncertain significance (Feb 16, 2023)
17-50376141-C-T		not specified	Likely benign (Nov 12, 2021)
17-50376153-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-50376186-C-T		not specified	Likely benign (Jul 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EME1	protein_coding	protein_coding	ENST00000393271	8	8264

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.50e-14	0.0656	125612	0	136	125748	0.000541

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0797	306	310	0.987	0.0000158	3795
Missense in Polyphen		80	76.728	1.0426		1018
Synonymous	0.422	115	121	0.951	0.00000634	1164
Loss of Function	0.630	23	26.5	0.868	0.00000130	304

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00116
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00167	0.00157
European (Non-Finnish)	0.000471	0.000440
Middle Eastern	0.0000544	0.0000544
South Asian	0.000555	0.000555
Other	0.000696	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Typical substrates include 3'- flap structures, replication forks and nicked Holliday junctions. May be required in mitosis for the processing of stalled or collapsed replication forks. {ECO:0000269|PubMed:12686547, ECO:0000269|PubMed:12721304, ECO:0000269|PubMed:14617801, ECO:0000269|PubMed:17289582}.
• Pathway: Fanconi anemia pathway - Homo sapiens (human);Homologous recombination - 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: 0.0974

Intolerance Scores

• loftool: 0.990
• rvis_EVS: 1
• rvis_percentile_EVS: 90.77

Haploinsufficiency Scores

• pHI: 0.0779
• hipred: N
• hipred_score: 0.147
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Eme1
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: resolution of meiotic recombination intermediates;double-strand break repair;replication fork processing;intra-S DNA damage checkpoint;interstrand cross-link repair;response to intra-S DNA damage checkpoint signaling;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nuclear chromatin;nucleoplasm;nuclear heterochromatin;nucleolus;Holliday junction resolvase complex
• Molecular function: DNA binding;endodeoxyribonuclease activity;protein binding;crossover junction endodeoxyribonuclease activity;metal ion binding