ANKMY1

Summary

ANKMY1 (ankyrin repeat and MYND domain containing 1, HGNC:20987) is a protein-coding gene on chromosome 2q37.3, encoding Ankyrin repeat and MYND domain-containing protein 1 (Q9P2S6).

Predicted to enable zinc ion binding activity.

Source: NCBI Gene 51281 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 260 total — 1 pathogenic
• MANE Select transcript: NM_001282771

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:20987
Approved symbol	ANKMY1
Name	ankyrin repeat and MYND domain containing 1
Location	2q37.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20499, ZMYND13
Ensembl gene	ENSG00000144504
Ensembl biotype	protein_coding
OMIM	620842
Entrez	51281

Gene structure

Transcript identifiers

Ensembl transcripts: 32 — 20 protein_coding, 7 retained_intron, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

ENST00000272972, ENST00000361678, ENST00000373318, ENST00000391988, ENST00000401804, ENST00000403283, ENST00000405002, ENST00000405523, ENST00000406958, ENST00000407275, ENST00000411765, ENST00000418505, ENST00000418708, ENST00000441168, ENST00000443318, ENST00000459901, ENST00000462004, ENST00000464991, ENST00000477316, ENST00000480230, ENST00000484526, ENST00000489677, ENST00000496300, ENST00000699162, ENST00000858016, ENST00000858017, ENST00000858018, ENST00000858019, ENST00000858020, ENST00000858021, ENST00000858022, ENST00000959624

RefSeq mRNA: 29 — MANE Select: NM_001282771 NM_001282771, NM_001282780, NM_001282781, NM_001308375, NM_001354023, NM_001354024, NM_001354026, NM_001393462, NM_001393463, NM_001393464, NM_001393465, NM_001393466, NM_001393467, NM_001393468, NM_001393469, NM_001393470, NM_001393471, NM_001393472, NM_001393475, NM_001393476, NM_001393477, NM_001393479, NM_001393480, NM_001393481, NM_001393482, NM_001393483, NM_001393484, NM_016552, NM_017844

CCDS: CCDS2535, CCDS2536, CCDS63184, CCDS63185, CCDS74681, CCDS77551, CCDS86929

Canonical transcript exons

ENST00000401804 — 18 exons

Exon	Start	End
ENSE00000965491	240526229	240526445
ENSE00001560243	240557881	240557988
ENSE00002218124	240520362	240520533
ENSE00002239444	240512802	240512942
ENSE00003486768	240554866	240555055
ENSE00003589256	240529037	240529509
ENSE00003632585	240557190	240557352
ENSE00003659389	240552914	240553057
ENSE00003712298	240507560	240507691
ENSE00003713474	240499958	240500123
ENSE00003717250	240511861	240512001
ENSE00003717378	240482183	240482261
ENSE00003720351	240509348	240509455
ENSE00003731547	240523885	240524381
ENSE00003743821	240480937	240481097
ENSE00003749053	240479422	240479655
ENSE00003752534	240500452	240500565
ENSE00003791352	240525685	240525849

Expression profiles

Bgee: expression breadth ubiquitous, 191 present calls, max score 96.34.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.7077 / max 132.9220, expressed in 1751 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
34833	7.2357	1664
34832	2.1772	1153
34831	0.1945	75
34830	0.1004	46

Top tissues by expression

266 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	96.34	gold quality
right testis	UBERON:0004534	92.69	gold quality
left testis	UBERON:0004533	92.65	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	90.59	gold quality
granulocyte	CL:0000094	90.42	gold quality
testis	UBERON:0000473	89.89	gold quality
sural nerve	UBERON:0015488	85.71	gold quality
monocyte	CL:0000576	83.27	gold quality
leukocyte	CL:0000738	82.77	gold quality
bronchial epithelial cell	CL:0002328	82.74	gold quality
endocervix	UBERON:0000458	82.74	gold quality
epithelium of bronchus	UBERON:0002031	82.73	gold quality
mucosa of transverse colon	UBERON:0004991	82.68	gold quality
mononuclear cell	CL:0000842	82.63	gold quality
lower esophagus mucosa	UBERON:0035834	82.35	gold quality
right hemisphere of cerebellum	UBERON:0014890	82.20	gold quality
bone marrow cell	CL:0002092	82.12	gold quality
bronchus	UBERON:0002185	82.07	gold quality
cerebellar cortex	UBERON:0002129	81.84	gold quality
cerebellar hemisphere	UBERON:0002245	81.83	gold quality
right ovary	UBERON:0002118	81.77	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	81.76	gold quality
left ovary	UBERON:0002119	81.71	gold quality
body of pancreas	UBERON:0001150	81.62	gold quality
spleen	UBERON:0002106	81.60	gold quality
skin of leg	UBERON:0001511	81.52	gold quality
blood	UBERON:0000178	81.45	gold quality
ectocervix	UBERON:0012249	81.34	gold quality
skin of abdomen	UBERON:0001416	81.22	gold quality
left uterine tube	UBERON:0001303	81.15	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	9.65

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting ANKMY1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-18A-5P	99.29	71.05	806
HSA-MIR-18B-5P	99.29	71.05	806
HSA-MIR-4735-3P	99.14	69.85	777
HSA-MIR-4736	97.96	65.89	1287
HSA-MIR-6894-3P	96.73	65.64	798
HSA-MIR-6762-5P	96.55	64.62	972
HSA-MIR-6845-5P	96.55	64.65	969
HSA-MIR-4737	89.94	65.03	82

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	ankmy1	ENSDARG00000062702
mus_musculus	Ankmy1	ENSMUSG00000034212
rattus_norvegicus	Ankmy1	ENSRNOG00000048567

Protein

Protein identifiers

Ankyrin repeat and MYND domain-containing protein 1 — Q9P2S6 (reviewed: Q9P2S6)

Alternative names: Testis-specific ankyrin-like protein 1, Zinc finger MYND domain-containing protein 13

All UniProt accessions (13): Q9P2S6, A0A8V8TPK4, B5MBY4, C9J5V7, C9JGS7, C9JZ56, H7BYI0, H7BYZ8, H7C254, J3KPY5, J3KQ07, J3KQ21, Q6GPI0

Isoforms (4)

UniProt ID	Names	Canonical?
Q9P2S6-1	1	yes
Q9P2S6-2	2
Q9P2S6-3	3
Q9P2S6-4	4

RefSeq proteins (28): NP_001269700, NP_001269709, NP_001269710, NP_001295304, NP_001340952, NP_001340953, NP_001340955, NP_001380391, NP_001380392, NP_001380393, NP_001380394, NP_001380395, NP_001380396, NP_001380397, NP_001380398, NP_001380399, NP_001380400, NP_001380401, NP_001380404, NP_001380405, NP_001380406, NP_001380408, NP_001380409, NP_001380410, NP_001380411, NP_001380412, NP_057636, NP_060314 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002110	Ankyrin_rpt	Repeat
IPR002893	Znf_MYND	Domain
IPR003409	MORN	Repeat
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR053064	Ankyrin-MYND_domain-protein	Family

Pfam: PF01753, PF02493, PF12796

UniProt features (32 total): repeat 10, binding site 8, splice variant 5, sequence variant 5, sequence conflict 2, chain 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P2S6-F1	78.09	0.45

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (8): 880; 883; 894; 897; 903; 907; 916; 920

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 52 (showing top): DODD_NASOPHARYNGEAL_CARCINOMA_DN, MODULE_49, MIKKELSEN_MEF_ICP_WITH_H3K27ME3, RATTENBACHER_BOUND_BY_CELF1, PTEN_DN.V2_UP, TGFB_UP.V1_DN, CBX5_TARGET_GENES, CDC5L_TARGET_GENES, CHAF1B_TARGET_GENES, E2F5_TARGET_GENES, ZFP3_TARGET_GENES, ZFP91_TARGET_GENES, ZNF410_TARGET_GENES, ZNF711_TARGET_GENES, ZNF766_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
binding	1
cation binding	1

Protein interactions and networks

STRING

490 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ANKMY1	MKRN2OS	H3BPM6	621
ANKMY1	THAP4	Q8WY91	562
ANKMY1	ZAR1	Q86SH2	473
ANKMY1	ZNF227	Q86WZ6	458
ANKMY1	FARP2	O94887	443
ANKMY1	SERP2	Q8N6R1	434
ANKMY1	PAX9	P55771	422
ANKMY1	STK25	O00506	421
ANKMY1	DTYMK	P23919	419
ANKMY1	RTP5	Q14D33	418
ANKMY1	NUCB1	Q02818	400
ANKMY1	MAB21L4	Q08AI8	398
ANKMY1	EVI5L	Q96CN4	396
ANKMY1	RNPEPL1	Q9HAU8	395
ANKMY1	FOXN1	O15353	375

IntAct

0 interactions, top by confidence:

BioGRID (5): ANKMY1 (Affinity Capture-RNA), RBPMS (Two-hybrid), ANKMY1 (Affinity Capture-MS), ANKMY1 (Affinity Capture-RNA), GOT2 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A1L3L1, A2RT67, A3KPW7, A4IIA7, A8C750, A8C752, D2HNY3, E1BGQ2, E1C3P4, Q08CL8, Q08DZ8, Q0IHB3, Q149N8, Q1RMU2, Q1RMZ1, Q3MJ13, Q3T1H6, Q5F3F2, Q5RED8, Q5VVJ2, Q5ZJ87, Q66J91, Q69Z66, Q6AYF5, Q6DE97, Q6GR37, Q6P1E7, Q6PNC0, Q6YHU6, Q7TPQ3, Q8BKW4, Q8BXK4, Q8IWR0, Q8IYF3, Q8IZE3, Q8K2I9, Q8NA31, Q8NEN0, Q8NFZ0, Q96EW2

Diamond homologs: Q8C0W1, Q9P2S6, Q9UU77, A2AQH4, A6NEL2, F1MJR8, G3I6Z6, O14974, O35516, P25631, P46531, Q01705, Q04721, Q07008, Q07E17, Q09YI3, Q09YJ5, Q09YN0, Q10728, Q1RJ94, Q1RJN6, Q2M3V2, Q2QL84, Q2QLA4, Q2QLC6, Q2QLH1, Q337A0, Q38898, Q54HW1, Q55FM5, Q5H9F3, Q5RCK5, Q61982, Q810B6, Q86WC6, Q8IWB6, Q91ZU0, Q93Z30, Q9BGT9, Q9BZL4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

260 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	199
Likely benign	21
Benign	4

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2425085	NC_000002.11:g.(?236403331)(242801596_?)del	Pathogenic

SpliceAI

4392 predictions. Top by Δscore:

Variant	Effect	Δscore
2:240480932:CCTA:C	donor_loss	1.0000
2:240480933:CTACC:C	donor_loss	1.0000
2:240480934:TA:T	donor_loss	1.0000
2:240480935:A:AC	donor_gain	1.0000
2:240480935:A:AT	donor_loss	1.0000
2:240480936:C:CC	donor_gain	1.0000
2:240480936:CCGAT:C	donor_loss	1.0000
2:240481096:TT:T	acceptor_gain	1.0000
2:240481098:C:CC	acceptor_gain	1.0000
2:240499952:GCTCA:G	donor_loss	1.0000
2:240499953:CTCA:C	donor_loss	1.0000
2:240499954:TCA:T	donor_loss	1.0000
2:240499955:CA:C	donor_loss	1.0000
2:240499956:A:C	donor_loss	1.0000
2:240499957:CCT:C	donor_gain	1.0000
2:240499957:CCTCT:C	donor_gain	1.0000
2:240500447:CCTA:C	donor_loss	1.0000
2:240500448:CTA:C	donor_loss	1.0000
2:240500449:TACCT:T	donor_loss	1.0000
2:240500450:ACC:A	donor_loss	1.0000
2:240500561:TCAAT:T	acceptor_gain	1.0000
2:240500562:CAAT:C	acceptor_gain	1.0000
2:240500562:CAATC:C	acceptor_gain	1.0000
2:240500565:TCTG:T	acceptor_loss	1.0000
2:240500566:C:A	acceptor_loss	1.0000
2:240500566:C:CC	acceptor_gain	1.0000
2:240500567:T:A	acceptor_loss	1.0000
2:240512938:CTCAG:C	acceptor_gain	1.0000
2:240512939:TCAGC:T	acceptor_loss	1.0000
2:240512941:AG:A	acceptor_gain	1.0000

AlphaMissense

6782 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:240481076:G:C	C880W	0.995
2:240481078:A:G	C880R	0.995
2:240481079:G:C	F879L	0.995
2:240481079:G:T	F879L	0.995
2:240481081:A:G	F879L	0.995
2:240500478:C:G	D783H	0.994
2:240529434:A:G	W97R	0.994
2:240529434:A:T	W97R	0.994
2:240481036:A:G	C894R	0.993
2:240481077:C:T	C880Y	0.993
2:240481062:C:G	R885P	0.992
2:240481009:A:G	C903R	0.991
2:240481063:G:T	R885S	0.991
2:240500477:T:A	D783V	0.991
2:240526333:C:G	A267P	0.991
2:240481027:A:G	C897R	0.990
2:240481065:C:T	G884D	0.990
2:240481069:A:G	C883R	0.990
2:240480997:A:G	C907R	0.989
2:240500023:A:G	L825P	0.989
2:240529439:C:T	G95E	0.989
2:240552983:G:C	F48L	0.989
2:240552983:G:T	F48L	0.989
2:240552985:A:G	F48L	0.989
2:240500477:T:G	D783A	0.988
2:240529440:C:A	G95W	0.988
2:240553054:A:C	Y25D	0.987
2:240481007:G:C	C903W	0.986
2:240481068:C:G	C883S	0.986
2:240481069:A:T	C883S	0.986

dbSNP variants (sampled 300 via entrez): RS1000003999 (2:240491813 A>C), RS1000007892 (2:240470942 G>A,T), RS1000030916 (2:240550692 G>A), RS1000046757 (2:240529412 T>C), RS1000074620 (2:240487696 T>C), RS1000098184 (2:240491504 C>T), RS1000129513 (2:240469737 C>G,T), RS1000145106 (2:240527813 T>C), RS1000148174 (2:240524193 C>G,T), RS1000153929 (2:240469605 G>A), RS1000183052 (2:240505352 C>T), RS1000230822 (2:240543992 T>C), RS1000254004 (2:240513784 G>A,C), RS1000260964 (2:240560054 T>C), RS1000278038 (2:240497967 C>G)

Disease associations

OMIM: gene MIM:620842 | disease phenotypes: MIM:158810

GenCC curated gene-disease

Mondo (1): Bethlem myopathy 1A (MONDO:0024530)

Orphanet (1): Bethlem muscular dystrophy (Orphanet:610)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST001335_9	Mean platelet volume	2.000000e-11
GCST005024_65	Pursuit maintenance gain	9.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008433	pursuit maintenance gain measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases expression	2
Arsenic	affects methylation, decreases expression, increases abundance	2
Benzo(a)pyrene	affects methylation, increases methylation	2
Smoke	decreases expression, increases abundance, increases expression	2
triphenyl phosphate	affects expression	1
bisphenol A	affects cotreatment, increases methylation	1
beta-lapachone	increases expression	1
arsenite	increases methylation	1
sodium arsenite	decreases expression, increases abundance	1
ferrous chloride	decreases expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
jinfukang	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Cisplatin	increases expression, affects cotreatment	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Succimer	affects cotreatment, increases expression	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Particulate Matter	increases abundance, increases expression	1
Magnetite Nanoparticles	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

1 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT04020159	Not specified	UNKNOWN	Global Registry for COL6-related Dystrophies