ZMYM1

Summary

ZMYM1 (zinc finger MYM-type containing 1, HGNC:26253) is a protein-coding gene on chromosome 1p34.3, encoding Zinc finger MYM-type protein 1 (Q5SVZ6).

Predicted to enable protein dimerization activity and zinc ion binding activity. Predicted to be located in nucleus.

Source: NCBI Gene 79830 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 139 total
• MANE Select transcript: NM_024772

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26253
Approved symbol	ZMYM1
Name	zinc finger MYM-type containing 1
Location	1p34.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23151, MYM
Ensembl gene	ENSG00000197056
Ensembl biotype	protein_coding
Entrez	79830

Gene structure

Transcript identifiers

Ensembl transcripts: 28 — 22 protein_coding, 6 protein_coding_CDS_not_defined

ENST00000359858, ENST00000373329, ENST00000373330, ENST00000417119, ENST00000463393, ENST00000466390, ENST00000475654, ENST00000476269, ENST00000488455, ENST00000611874, ENST00000650449, ENST00000905955, ENST00000905956, ENST00000905957, ENST00000905958, ENST00000931028, ENST00000931029, ENST00000931030, ENST00000931031, ENST00000931032, ENST00000931033, ENST00000931034, ENST00000931035, ENST00000931036, ENST00000964798, ENST00000964799, ENST00000964800, ENST00000964801

RefSeq mRNA: 6 — MANE Select: NM_024772 NM_001289088, NM_001289089, NM_001289090, NM_001289091, NM_001319955, NM_024772

CCDS: CCDS41302

Canonical transcript exons

ENST00000359858 — 10 exons

Exon	Start	End
ENSE00001460285	35112977	35115859
ENSE00001460290	35079385	35079442
ENSE00003477630	35093914	35094083
ENSE00003498284	35097317	35097566
ENSE00003535611	35095819	35095891
ENSE00003697440	35110294	35110447
ENSE00003698994	35104295	35104469
ENSE00003699331	35112087	35112130
ENSE00003700711	35111772	35111912
ENSE00003701996	35104557	35104769

Expression profiles

Bgee: expression breadth ubiquitous, 231 present calls, max score 88.33.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.4533 / max 279.7789, expressed in 1758 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
2084	11.4533	1758

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.33	gold quality
adrenal tissue	UBERON:0018303	87.72	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.17	gold quality
calcaneal tendon	UBERON:0003701	85.78	gold quality
ventricular zone	UBERON:0003053	83.23	gold quality
stromal cell of endometrium	CL:0002255	80.59	gold quality
ganglionic eminence	UBERON:0004023	79.54	gold quality
cortical plate	UBERON:0005343	78.96	gold quality
esophagus squamous epithelium	UBERON:0006920	78.45	gold quality
islet of Langerhans	UBERON:0000006	78.15	gold quality
visceral pleura	UBERON:0002401	77.89	gold quality
choroid plexus epithelium	UBERON:0003911	77.86	gold quality
monocyte	CL:0000576	77.80	gold quality
right ovary	UBERON:0002118	77.77	gold quality
mononuclear cell	CL:0000842	77.65	gold quality
hair follicle	UBERON:0002073	77.65	silver quality
leukocyte	CL:0000738	77.59	gold quality
tibia	UBERON:0000979	77.46	gold quality
parietal pleura	UBERON:0002400	77.46	gold quality
rectum	UBERON:0001052	77.40	gold quality
ovary	UBERON:0000992	77.21	gold quality
endometrium	UBERON:0001295	77.16	gold quality
left ovary	UBERON:0002119	77.16	gold quality
gingival epithelium	UBERON:0001949	77.12	silver quality
ectocervix	UBERON:0012249	76.89	gold quality
pleura	UBERON:0000977	76.84	gold quality
tonsil	UBERON:0002372	76.78	gold quality
body of uterus	UBERON:0009853	76.67	gold quality
esophagus mucosa	UBERON:0002469	76.36	gold quality
right uterine tube	UBERON:0001302	76.31	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-99795	no	119.07
E-ANND-3	no	5.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting ZMYM1, 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-6748-5P	100.00	65.81	1057
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-485-3P	99.98	70.68	1585
HSA-MIR-539-3P	99.98	70.74	1616
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-1208	99.70	68.28	1533

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-240b21.2	ENSDARG00000068279
mus_musculus	Zmym1	ENSMUSG00000043872
rattus_norvegicus	Zmym1	ENSRNOG00000013855

Paralogs (18): GTF2IRD1 (ENSG00000006704), ZMYM2 (ENSG00000121741), ZMYM5 (ENSG00000132950), THAP12 (ENSG00000137492), ZMYM4 (ENSG00000146463), ZMYM3 (ENSG00000147130), ZMYM6 (ENSG00000163867), KIAA1958 (ENSG00000165185), GTF2IRD2B (ENSG00000174428), EPM2AIP1 (ENSG00000178567), GTF2IRD2 (ENSG00000196275), QRICH1 (ENSG00000198218), FAM200C (ENSG00000221886), FAM200A (ENSG00000221909), SCAND3 (ENSG00000232040), ZBED5 (ENSG00000236287), FAM200B (ENSG00000237765), GTF2I (ENSG00000263001)

Protein

Protein identifiers

Zinc finger MYM-type protein 1 — Q5SVZ6 (reviewed: Q5SVZ6)

All UniProt accessions (2): Q5SVZ6, Q5SVZ7

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

RefSeq proteins (6): NP_001276017, NP_001276018, NP_001276019, NP_001276020, NP_001306884, NP_079048* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008906	HATC_C_dom	Domain
IPR010507	Znf_MYM	Domain
IPR011017	TRASH_dom	Domain
IPR012337	RNaseH-like_sf	Homologous_superfamily
IPR025398	RNase-like_ZMYM1	Domain
IPR051284	ZnF_MYMT-QRICH1	Family

Pfam: PF05699, PF06467, PF14291, PF24900

UniProt features (14 total): zinc finger region 5, sequence variant 3, cross-link 2, compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5SVZ6-F1	67.23	0.19

Functional residue map

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

Post-translational modifications (2): 284, 25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 87 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, MODULE_285, FISCHER_G2_M_CELL_CYCLE, chr1p34, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, FISCHER_DREAM_TARGETS, YAMAZAKI_TCEB3_TARGETS_DN, MARSON_BOUND_BY_E2F4_UNSTIMULATED, KIM_WT1_TARGETS_DN, GOMF_PROTEIN_DIMERIZATION_ACTIVITY, BOCHKIS_FOXA2_TARGETS, GEORGES_TARGETS_OF_MIR192_AND_MIR215, HAMAI_APOPTOSIS_VIA_TRAIL_UP, WHITFIELD_CELL_CYCLE_G2_M, HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_UP

GO Biological Process (0):

GO Molecular Function (3): zinc ion binding (GO:0008270), protein dimerization activity (GO:0046983), metal ion binding (GO:0046872)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transition metal ion binding	1
protein binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

822 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZMYM1	RCOR1	Q9UKL0	593
ZMYM1	ELAVL1	Q15717	578
ZMYM1	CTBP1	Q13363	576
ZMYM1	METTL3	Q86U44	570
ZMYM1	KDM1A	O60341	549
ZMYM1	METTL14	Q9HCE5	448
ZMYM1	HDGF	P51858	447
ZMYM1	WTAP	Q15007	434
ZMYM1	YTHDF1	Q9BYJ9	431
ZMYM1	ALKBH5	Q6P6C2	420
ZMYM1	VIRMA	Q69YN4	400
ZMYM1	YTHDF2	Q9Y5A9	398
ZMYM1	TMEM35B	Q8NCS4	396
ZMYM1	RBM15	Q96T37	384
ZMYM1	IGF2BP2	Q9Y6M1	373

IntAct

84 interactions, top by confidence:

A	B	Type	Score
RNF146	TNKS	psi-mi:“MI:0914”(association)	0.790
CAMK2A	CAMK2G	psi-mi:“MI:0914”(association)	0.730
GPR156	PLD2	psi-mi:“MI:0914”(association)	0.640
ERP44	MEX3A	psi-mi:“MI:0914”(association)	0.530
TRIM44	ODAD3	psi-mi:“MI:0914”(association)	0.530
PSG9	CCDC85C	psi-mi:“MI:0914”(association)	0.530
XAGE1A	THAP12	psi-mi:“MI:0914”(association)	0.530
SALL2	GFPT2	psi-mi:“MI:0914”(association)	0.530
FHL5	ZMYM6	psi-mi:“MI:0914”(association)	0.530
ELP2	DNAJA2	psi-mi:“MI:0914”(association)	0.530
USP7	ZMYM1	psi-mi:“MI:0407”(direct interaction)	0.440
Ctcf	RPL36A	psi-mi:“MI:0915”(physical association)	0.400
ZMYM1	ABLIM1	psi-mi:“MI:0914”(association)	0.350
SKA1	ILVBL	psi-mi:“MI:0914”(association)	0.350
AURKA	CTNNB1	psi-mi:“MI:0914”(association)	0.350
Ttll12	TPM1	psi-mi:“MI:0914”(association)	0.350
L1TD1	PPP1R12C	psi-mi:“MI:0914”(association)	0.350
Prdx1	TRIO	psi-mi:“MI:0914”(association)	0.350
Chmp3	DTL	psi-mi:“MI:0914”(association)	0.350
RNASEH2B	SAP18	psi-mi:“MI:0914”(association)	0.350
Chmp4c	SF1	psi-mi:“MI:0914”(association)	0.350
HDAC6	GLOD5	psi-mi:“MI:0914”(association)	0.350
GAR1	TAF1	psi-mi:“MI:0914”(association)	0.350
VAPA		psi-mi:“MI:0914”(association)	0.350

BioGRID (107): ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS), ZMYM1 (Affinity Capture-MS)

ESM2 similar proteins: A3KMX0, A4IFA3, A4IGY9, A4Z943, A4Z944, B8QB46, D2EAC2, E1C2V1, O43422, O60290, P10911, P35125, P86452, Q13075, Q2NKX8, Q3UPF5, Q49AG3, Q5FWF4, Q5SVZ6, Q5T890, Q5TKR9, Q6DJS0, Q6EKJ0, Q6R2W3, Q6YI93, Q7Z2W4, Q80WE4, Q86UP8, Q86VD1, Q8BZ21, Q8N8K9, Q8QMP8, Q8TDB6, Q8WML3, Q92794, Q96JM7, Q96JS3, Q99388, Q99NI3, Q9CUX1

Diamond homologs: A2A791, A6QPH9, O95789, Q0P5J0, Q14202, Q2TAL8, Q3U2E2, Q3UA37, Q4R3D6, Q5RDJ2, Q5SVZ6, Q5VZL5, Q9CU65, Q9JLM4, Q9UBW7, Q9UJ78, A4Z943, A4Z944, A4Z945, P0CF97, Q49AG3, Q4R6P1, Q6R2W3, Q8IZ13, Q8TCP9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	118
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1918 predictions. Top by Δscore:

Variant	Effect	Δscore
1:35094084:G:GG	donor_gain	1.0000
1:35104293:A:AG	acceptor_gain	1.0000
1:35104294:G:GG	acceptor_gain	1.0000
1:35104294:GA:G	acceptor_gain	1.0000
1:35104294:GAGAC:G	acceptor_gain	1.0000
1:35104470:G:GG	donor_gain	1.0000
1:35110290:ACAG:A	acceptor_loss	1.0000
1:35110291:CA:C	acceptor_loss	1.0000
1:35110292:A:AC	acceptor_loss	1.0000
1:35110292:A:AG	acceptor_gain	1.0000
1:35110293:G:GA	acceptor_gain	1.0000
1:35110327:A:AG	acceptor_gain	1.0000
1:35110328:A:G	acceptor_gain	1.0000
1:35110427:C:G	donor_gain	1.0000
1:35110443:TTCAG:T	donor_loss	1.0000
1:35110444:TCAG:T	donor_loss	1.0000
1:35110445:CAGG:C	donor_loss	1.0000
1:35110446:AGGTA:A	donor_loss	1.0000
1:35110447:GG:G	donor_loss	1.0000
1:35110448:GTA:G	donor_loss	1.0000
1:35110449:T:G	donor_loss	1.0000
1:35111771:GTA:G	acceptor_gain	1.0000
1:35111771:GTAA:G	acceptor_gain	1.0000
1:35111908:ACAAG:A	donor_loss	1.0000
1:35111909:CAAG:C	donor_loss	1.0000
1:35111910:AAG:A	donor_loss	1.0000
1:35111912:G:GC	donor_loss	1.0000
1:35111913:GTAA:G	donor_loss	1.0000
1:35111914:T:G	donor_loss	1.0000
1:35112085:A:AG	acceptor_gain	1.0000

AlphaMissense

7584 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:35114910:T:C	L1027P	0.991
1:35097412:T:C	C89R	0.986
1:35113610:G:C	A594P	0.986
1:35097481:T:C	F112L	0.985
1:35097483:C:A	F112L	0.985
1:35097483:C:G	F112L	0.985
1:35097414:T:G	C89W	0.984
1:35097550:T:C	C135R	0.984
1:35097552:T:G	C135W	0.984
1:35097412:T:A	C89S	0.983
1:35097413:G:C	C89S	0.983
1:35104374:T:C	C167R	0.982
1:35097421:T:A	C92S	0.981
1:35097422:G:C	C92S	0.981
1:35104376:T:G	C167W	0.980
1:35114918:T:G	Y1030D	0.980
1:35097484:T:C	C113R	0.979
1:35097550:T:A	C135S	0.979
1:35097551:G:C	C135S	0.979
1:35097413:G:A	C89Y	0.976
1:35097484:T:A	C113S	0.976
1:35097485:G:C	C113S	0.976
1:35097496:T:C	C117R	0.976
1:35114831:T:A	W1001R	0.975
1:35114831:T:C	W1001R	0.975
1:35114922:G:C	R1031P	0.975
1:35114741:G:A	G971R	0.973
1:35114741:G:C	G971R	0.973
1:35097486:C:G	C113W	0.972
1:35097561:C:G	C138W	0.972

dbSNP variants (sampled 300 via entrez): RS1000032360 (1:35064906 A>G), RS1000063030 (1:35080283 C>T), RS1000122302 (1:35087301 T>A), RS1000158729 (1:35084036 A>G), RS1000175368 (1:35105371 T>C), RS1000191077 (1:35101637 G>A), RS1000307518 (1:35076709 G>T), RS1000332236 (1:35092658 C>T), RS1000336139 (1:35099516 T>C), RS1000584865 (1:35108622 G>A), RS1000594392 (1:35082198 G>C,T), RS1000639807 (1:35064100 T>C,G), RS1000701272 (1:35118798 A>G), RS1000701457 (1:35061508 G>A), RS1000711363 (1:35077034 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST004751_3	Serum uric acid levels in response to allopurinol in gout	4.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004761	uric acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

26 total (human), top 26 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	decreases expression, affects expression, increases abundance	2
TAK-243	increases sumoylation	1
bufotalin	increases expression	1
testosterone enanthate	affects expression	1
triphenyl phosphate	affects expression	1
arsenite	affects binding, decreases reaction	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
sodium arsenite	decreases expression	1
manganese chloride	increases abundance, increases expression	1
di-n-butylphosphoric acid	affects expression	1
jinfukang	decreases expression	1
Acetaminophen	increases expression	1
Benzo(a)pyrene	affects methylation	1
Cisplatin	decreases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Manganese	increases abundance, increases expression	1
Ozone	affects expression, increases abundance	1
Testosterone	decreases expression	1
Thiram	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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