MEI1

protein-coding

meiotic double-stranded break formation protein 1, the group of Armadillo like helical domain containing

Gene summary

Predicted to be involved in meiosis I. Predicted to act upstream of or within germ cell development; meiotic nuclear division; and meiotic spindle organization. Implicated in gestational trophoblastic neoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_152513.4

Inheritance

ClinVar variants

P:16U:164B:40

Top phenotype

Hydatidiform mole, recurrent, 3

gnomAD constraint

pLI —, LoF o/e 0.47

Max pathogenic AF

—

Genomic locus

chr22:41,699,503-41,799,456

External References & Databases

Ensembl (ENSG00000167077)

Transcript & Mutation Effects

hg38 • Region Span ~100.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

complete hydatidiform moleSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0016785

Submitter: Orphanet

hydatidiform mole, recurrent, 3STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032746

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Hydatidiform mole, recurrent, 3AR

Manifestation: Obstetric; Oncologic

Intervention: Obstetric; Oncologic

Rationale: Women are likely to have pregnancies with hydatidiform moles, and awareness may allow reproductive planning and/or surveillance measures, which may allow early detection and treatment

Refs: 30388401

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MEI1 variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 164

MEI1-related disorderTotal: 29

not providedTotal: 21

Hydatidiform mole, recurrent, 3Total: 14

OOCYTE/ZYGOTE/EMBRYO MATURATION ARREST 26Total: 6

SPERMATOGENIC FAILURE 103Total: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152513.4. 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			4 clinvar	15 clinvar	4 clinvar	23
missense	1 clinvar	1 clinvar	153 clinvar	15 clinvar	6 clinvar	176
nonsense	1 clinvar	2 clinvar	3 clinvar			6
start loss						0
frameshift	4 clinvar	1 clinvar				5
splice donor/acceptor (+/-2bp)	3 clinvar	3 clinvar	4 clinvar			10
Total	9	7	164	30	10	220

Highest pathogenic variant AF is 0.00043196892

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152513.4	RefSeq	NP_689726.3	31	MANE Select
ENST00000401548.8	Ensembl	ENSP00000384115.3	31	MANE Select
ENST00000403492.5	Ensembl	ENSP00000385298.1	7	Standard
ENST00000423900.1	Ensembl	ENSP00000410973.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

male meiosis I
spermatid development
meiotic telomere clustering

Cellular Component

cell

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000401548
Coding exons: 31
Length: 99958
Individuals with no LoFs: 124638
Homozygous LoFs: 0
Heterozygous LoFs: 127
Defined: 124765
p: 0.000509

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.872	608	672	0.905	0.0000349	8205
Missense (PolyPhen)		210	258.92	0.81105		3346
Synonymous	0.135	280	283	0.990	0.0000148	2597
Loss of Function	3.95	30	64.1	0.468	0.00000322	758

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.00094	0.00093	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.0010	0.0010	notable
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00045	0.00044	rare
South Asian	0.00048	0.00046	rare
Other	0.00084	0.00082	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Required for normal meiotic chromosome synapsis. May be involved in the formation of meiotic double-strand breaks (DSBs) in spermatocytes (By similarity). {ECO:0000250|UniProtKB:Q9D4I2}.;

Intolerance Scores

LoFtool: 0.938
RVIS EVS: -0.46
RVIS percentile EVS: 23.7

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.129

Gene Damage Prediction

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