ZMYND12

protein-coding

zinc finger MYND-type containing 12, the group of Zinc fingers MYND-type

Gene summary

Predicted to enable zinc ion binding activity. Involved in sperm axoneme assembly. Located in sperm flagellum. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_032257.5

Inheritance

—

ClinVar variants

U:50B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr1:42,430,329-42,456,253

External References & Databases

Ensembl (ENSG00000066185)

Transcript & Mutation Effects

hg38 • Region Span ~25.9 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 ZMYND12 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 50

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032257.5. 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			1 clinvar	3 clinvar	1 clinvar	5
missense			46 clinvar	3 clinvar		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	50	6	1	57

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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_032257.5	RefSeq	NP_115633.3	8	MANE Select
ENST00000372565.8	Ensembl	ENSP00000361646.3	8	MANE Select
NM_001146192.2	RefSeq	NP_001139664.1	6	Standard
ENST00000461083.1	Ensembl	ENSP00000482602.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000372565
Coding exons: 8
Length: 25939
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125748
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.706	172	200	0.860	0.0000106	2366
Missense (PolyPhen)		35	42.797	0.81782		462
Synonymous	0.848	67	76.4	0.877	0.00000379	702
Loss of Function	1.87	10	18.7	0.534	9.40e-7	221

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00016	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00019	0.00018	rare
South Asian	0	0.0	absent
Other	0.00035	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.640
RVIS EVS: 0.31
RVIS percentile EVS: 72.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0966

Gene Damage Prediction

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