MEIG1

protein-coding

meiosis/spermiogenesis associated 1

Gene summary

Predicted to be involved in cell differentiation. Predicted to act upstream of or within intracellular protein localization; manchette assembly; and sperm axoneme assembly. Predicted to be located in cytosol and manchette. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001080836.3

Inheritance

—

ClinVar variants

U:19

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.06

Max pathogenic AF

—

Genomic locus

chr10:14,959,388-14,988,050

External References & Databases

Ensembl (ENSG00000197889)

Transcript & Mutation Effects

hg38 • Region Span ~28.7 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 MEIG1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080836.3. 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						0
missense			18 clinvar			18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	19	0	0	19

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080836.3	RefSeq	NP_001074305.1	2	MANE Select
ENST00000407572.6	Ensembl	ENSP00000384334.1	2	MANE Select
ENST00000378240.1	Ensembl	ENSP00000367486.1	2	Standard
ENST00000378240.2	Ensembl	ENSP00000367486.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatogenesis
cell differentiation

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000407572
Coding exons: 2
Length: 28612
Individuals with no LoFs: 125724
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125735
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.225	53	48.6	1.09	0.00000269	577
Missense (PolyPhen)		18	16.177	1.1127		200
Synonymous	0.113	15	15.6	0.964	8.48e-7	140
Loss of Function	-0.117	5	4.72	1.06	1.99e-7	59

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000079	0.000079	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Essential for spermiogenesis. {ECO:0000250}.;

Recessive Scores

pRec: 0.0955

Intolerance Scores

LoFtool: 0.636
RVIS EVS: 0.35
RVIS percentile EVS: 73.97

Essentials

Essential (CRISPR): N
Indispensability pred.: E
Indispensability score: 0.510

Gene Damage Prediction

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