ANKMY2

protein-coding

ankyrin repeat and MYND domain containing 2, the group of Ankyrin repeat domain containing|Zinc fingers MYND-type

Gene summary

Predicted to enable enzyme binding activity and zinc ion binding activity. Predicted to be located in cilium. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020319.3

Inheritance

—

ClinVar variants

U:75

Top phenotype

High myopia

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr7:16,599,779-16,645,817

External References & Databases

Ensembl (ENSG00000106524)

Transcript & Mutation Effects

hg38 • Region Span ~46.0 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 ANKMY2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 67

High myopiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020319.3. 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			69 clinvar			69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	75	0	0	75

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020319.3	RefSeq	NP_064715.1	10	MANE Select
ENST00000306999.7	Ensembl	ENSP00000303570.2	10	MANE Select
ENST00000447802.3	Ensembl	ENSP00000392259.1	9	Standard
ENST00000453623.5	Ensembl	ENSP00000410075.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
enzyme binding
metal ion binding

Cellular Component

cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306999
Coding exons: 10
Length: 46042
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 49
Defined: 125748
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.151	221	227	0.972	0.0000109	2912
Missense (PolyPhen)		56	64.242	0.87171		842
Synonymous	-0.215	84	81.5	1.03	0.00000420	794
Loss of Function	1.82	12	21.0	0.571	0.00000120	259

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00065	0.00064	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.000033	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in the trafficking of signaling proteins to the cilia. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.541
RVIS EVS: -0.02
RVIS percentile EVS: 52.09

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.475

Gene Damage Prediction

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