ANKMY1

Chr 2

ankyrin repeat and MYND domain containing 1

Also known as: ZMYND13

NCBI Gene: 51281 ENSG00000144504 UniProt: Q9P2S6 OMIM: 620842

ANKMY1 encodes a protein predicted to bind zinc ions, though its specific cellular function remains unclear. Mutations cause autosomal recessive developmental delays and intellectual disability, typically with onset in early childhood. The gene shows low constraint against loss-of-function variants, consistent with the recessive inheritance pattern observed in affected individuals.

OMIM ResearchSummary from RefSeq

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

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.21

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.21LOEUF

pLI 0.000

Z-score 0.44

OE 0.93 (0.71–1.21)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.26Z-score

OE missense 1.03 (0.96–1.10)

587 obs / 569.7 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.93 (0.71–1.21)

0≤0.351.4

Missense OE?1.03 (0.96–1.10)

0≤0.61.4

Synonymous OE?1.00

0≤1.21.6

LoF obs/exp: 38 / 41.0Missense obs/exp: 587 / 569.7Syn Z: 0.04

Background carrier burden — how many people carry a rare variant somewhere in ANKMY1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 27

1,639 rare PASS variants

Rare truncating (LoF)

1 in 310

277 rare PASS variants

Rare synonymous (reference)

1 in 58

657 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ANKMY1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 44	1 in 460
South Asian	~43k	1 in 23	1 in 210
Remaining (unassigned)	~30k	1 in 20	1 in 280
European (Finnish)	~27k	1 in 110	1 in 1,600
Admixed American	~22k	1 in 25	1 in 230
African / African American	~21k	1 in 24	1 in 210
East Asian	~20k	1 in 23	1 in 240
Ashkenazi Jewish	~13k	1 in 88	1 in 900
Middle Eastern	~2,884	1 in 27	1 in 280

Each group is summed over the variants that are rare in that group. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.