MAEL

protein-coding

maelstrom spermatogenic transposon silencer

Gene summary

Predicted to enable sequence-specific DNA binding activity. Predicted to be involved in male meiotic nuclear division; regulation of gene expression; and spermatogenesis. Predicted to act upstream of or within several processes, including homologous chromosome pairing at meiosis; intrinsic apoptotic signaling pathway in response to DNA damage; and regulation of gene expression. Predicted to be located in piP-body. Predicted to be active in P granule and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_032858.3

Inheritance

—

ClinVar variants

P:2U:41B:3

Top phenotype

Male infertility

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr1:166,975,582-167,022,214

External References & Databases

Ensembl (ENSG00000143194)

Transcript & Mutation Effects

hg38 • Region Span ~46.6 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 MAEL variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 41

not providedTotal: 2

Male infertilityTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032858.3. 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			40 clinvar	1 clinvar	2 clinvar	43
nonsense		1 clinvar				1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)		1 clinvar	1 clinvar			2
Total	0	2	41	1	2	46

Highest pathogenic variant AF is 0.0000095840915

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032858.3	RefSeq	NP_116247.1	12	MANE Select
ENST00000367872.9	Ensembl	ENSP00000356846.4	12	MANE Select
NM_001286377.2	RefSeq	NP_001273306.1	11	Standard
NM_001286378.2	RefSeq	NP_001273307.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
PIWI-interacting RNA (piRNA) biogenesis
Gene Silencing by RNA

Biological Process

negative regulation of transcription by RNA polymerase II
cell morphogenesis
synapsis
male meiotic nuclear division
multicellular organism development

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
sequence-specific DNA binding

Cellular Component

chromatin
XY body
nucleus
cytoplasm
autosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367872
Coding exons: 12
Length: 33106
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125748
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.959	196	238	0.825	0.0000125	2837
Missense (PolyPhen)		51	78.681	0.64818		901
Synonymous	-0.207	82	79.7	1.03	0.00000400	797
Loss of Function	3.16	10	28.1	0.356	0.00000170	295

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000088	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00016	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a central role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for the germline integrity. Acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons. Its association with piP- bodies suggests a participation in the secondary piRNAs metabolic process. Required for the localization of germ-cell factors to the meiotic nuage (By similarity). {ECO:0000250|UniProtKB:Q8BVN9}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.711
RVIS EVS: 0.11
RVIS percentile EVS: 61.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0360

Gene Damage Prediction

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