ANKMY1

protein-coding

ankyrin repeat and MYND domain containing 1, the group of Ankyrin repeat domain containing|Zinc fingers MYND-type

Gene summary

Predicted to enable zinc ion binding activity. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001282771.3

Inheritance

—

ClinVar variants

U:175B:25

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.93

Max pathogenic AF

—

Genomic locus

chr2:240,479,422-240,569,209

External References & Databases

Ensembl (ENSG00000144504)

Transcript & Mutation Effects

hg38 • Region Span ~89.8 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 ANKMY1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 174

not providedTotal: 6

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001282771.3. 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			6 clinvar	2 clinvar	3 clinvar	11
missense			164 clinvar	19 clinvar	1 clinvar	184
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	175	21	4	200

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 103 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001282771.3	RefSeq	NP_001269700.1	17	MANE Select
ENST00000401804.6	Ensembl	ENSP00000385887.1	17	MANE Select
NM_001282780.2	RefSeq	NP_001269709.1	13	Standard
NM_001282781.2	RefSeq	NP_001269710.1	16	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: ENST00000391987
Coding exons: 16
Length: 89788
Individuals with no LoFs: 125401
Homozygous LoFs: 0
Heterozygous LoFs: 347
Defined: 125748
p: 0.00138

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.257	587	570	1.03	0.0000348	6165
Missense (PolyPhen)		205	200.76	1.0211		2149
Synonymous	0.0389	247	248	0.997	0.0000168	1852
Loss of Function	0.440	38	41.0	0.926	0.00000201	478

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0026	0.0026	notable
Latino/Admixed American	0.00046	0.00038	rare
Ashkenazi Jewish	0.0018	0.0018	notable
East Asian	0.0032	0.0032	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.0011	0.0011	notable
South Asian	0.0026	0.0026	notable
Other	0.0012	0.0011	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.930
RVIS EVS: -0.23
RVIS percentile EVS: 37.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.147

Gene Damage Prediction

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