ZMYM5

Summary

ZMYM5 (zinc finger MYM-type containing 5, HGNC:13029) is a protein-coding gene on chromosome 13q12.11, encoding Zinc finger MYM-type protein 5 (Q9UJ78). Functions as a transcriptional regulator.

Predicted to enable zinc ion binding activity. Involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 9205 — RefSeq curated summary.

At a glance

• Gene–disease (curated): multiple congenital anomalies/dysmorphic syndrome (Limited, GenCC)
• GWAS associations: 3
• Clinical variants (ClinVar): 70 total
• MANE Select transcript: NM_001142684

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13029
Approved symbol	ZMYM5
Name	zinc finger MYM-type containing 5
Location	13q12.11
Locus type	gene with protein product
Status	Approved
Aliases	ZNF198L1, MYM
Ensembl gene	ENSG00000132950
Ensembl biotype	protein_coding
OMIM	616443
Entrez	9205

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 4 retained_intron

ENST00000337963, ENST00000382905, ENST00000382907, ENST00000382909, ENST00000467542, ENST00000495534, ENST00000535942, ENST00000854551, ENST00000854552, ENST00000854553, ENST00000854554, ENST00000923234, ENST00000923235, ENST00000954241, ENST00000954242

RefSeq mRNA: 3 — MANE Select: NM_001142684 NM_001039649, NM_001039650, NM_001142684

CCDS: CCDS31942, CCDS31943

Canonical transcript exons

ENST00000337963 — 8 exons

Exon	Start	End
ENSE00000994960	19862399	19862466
ENSE00001229583	19863450	19863649
ENSE00001541459	19823482	19825235
ENSE00001637679	19851689	19852190
ENSE00001795699	19851355	19851448
ENSE00003489413	19835477	19835689
ENSE00003517535	19838700	19838985
ENSE00003674283	19837656	19837821

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 94.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.6471 / max 118.9985, expressed in 1540 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
136324	1.7283	977
136323	1.3838	822
136322	0.8190	539
136321	0.7160	415

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	94.23	gold quality
secondary oocyte	CL:0000655	91.12	gold quality
oocyte	CL:0000023	90.78	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.77	gold quality
adrenal tissue	UBERON:0018303	87.59	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.98	gold quality
calcaneal tendon	UBERON:0003701	86.93	gold quality
nipple	UBERON:0002030	86.68	gold quality
ventricular zone	UBERON:0003053	86.52	gold quality
ganglionic eminence	UBERON:0004023	86.36	gold quality
cardia of stomach	UBERON:0001162	85.46	gold quality
cauda epididymis	UBERON:0004360	85.28	gold quality
monocyte	CL:0000576	85.24	gold quality
colonic epithelium	UBERON:0000397	85.02	gold quality
medial globus pallidus	UBERON:0002477	84.98	gold quality
corpus callosum	UBERON:0002336	84.87	gold quality
renal medulla	UBERON:0000362	84.79	gold quality
pylorus	UBERON:0001166	84.65	gold quality
mononuclear cell	CL:0000842	84.48	gold quality
inferior vagus X ganglion	UBERON:0005363	84.45	gold quality
superficial temporal artery	UBERON:0001614	84.40	gold quality
trabecular bone tissue	UBERON:0002483	84.39	gold quality
lower esophagus mucosa	UBERON:0035834	84.36	gold quality
leukocyte	CL:0000738	84.25	gold quality
gall bladder	UBERON:0002110	84.23	gold quality
globus pallidus	UBERON:0001875	84.17	gold quality
cortical plate	UBERON:0005343	84.06	gold quality
mucosa of paranasal sinus	UBERON:0005030	83.92	gold quality
right testis	UBERON:0004534	83.76	gold quality
endocervix	UBERON:0000458	83.74	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-CURD-112	no	2.57
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Zmym5	ENSMUSG00000040123
rattus_norvegicus	Zmym5	ENSRNOG00000029220

Paralogs (18): GTF2IRD1 (ENSG00000006704), ZMYM2 (ENSG00000121741), THAP12 (ENSG00000137492), ZMYM4 (ENSG00000146463), ZMYM3 (ENSG00000147130), ZMYM6 (ENSG00000163867), KIAA1958 (ENSG00000165185), GTF2IRD2B (ENSG00000174428), EPM2AIP1 (ENSG00000178567), GTF2IRD2 (ENSG00000196275), ZMYM1 (ENSG00000197056), QRICH1 (ENSG00000198218), FAM200C (ENSG00000221886), FAM200A (ENSG00000221909), SCAND3 (ENSG00000232040), ZBED5 (ENSG00000236287), FAM200B (ENSG00000237765), GTF2I (ENSG00000263001)

Protein

Protein identifiers

Zinc finger MYM-type protein 5 — Q9UJ78 (reviewed: Q9UJ78)

Alternative names: Zinc finger protein 198-like 1, Zinc finger protein 237

All UniProt accessions (1): Q9UJ78

UniProt curated annotations — full annotation on UniProt →

Function. Functions as a transcriptional regulator.

Subunit / interactions. Interacts (via N-terminal 120 amino acid region) with ETV5 (via C-terminal).

Subcellular location. Nucleus.

Isoforms (5)

UniProt ID	Names	Canonical?
Q9UJ78-4	4	yes
Q9UJ78-1	1
Q9UJ78-2	2
Q9UJ78-3	3
Q9UJ78-5	5

RefSeq proteins (3): NP_001034738, NP_001034739, NP_001136156* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010507	Znf_MYM	Domain
IPR011017	TRASH_dom	Domain
IPR051284	ZnF_MYMT-QRICH1	Family

Pfam: PF06467

UniProt features (35 total): cross-link 10, splice variant 7, zinc finger region 4, mutagenesis site 4, sequence variant 3, sequence conflict 3, chain 1, turn 1, strand 1, helix 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
2DAS	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UJ78-F1	60.82	0.17

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 (10): 225, 443, 455, 462, 552, 88, 91, 134, 149, 166

Mutagenesis-validated functional residues (4):

Position	Phenotype
112	abolishes interaction with etv5. abolished repression activity.
114	abolishes interaction with etv5. no effect on repression activity.
116	no effect on repression activity.
120	increases repression activity.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 139 (showing top): RNGTGGGC_UNKNOWN, MULLIGHAN_NPM1_SIGNATURE_3_UP, MODULE_255, MODULE_317, TTGGGAG_MIR150, BLALOCK_ALZHEIMERS_DISEASE_UP, AGTCAGC_MIR345, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN, PARENT_MTOR_SIGNALING_UP, GAL_LEUKEMIC_STEM_CELL_UP, MODULE_69, KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP, GOBP_NEGATIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II, JOHNSTONE_PARVB_TARGETS_3_DN, GOBP_NEGATIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS

GO Biological Process (1): negative regulation of transcription by RNA polymerase II (GO:0000122)

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), 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
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
negative regulation of DNA-templated transcription	1
transition metal ion binding	1
binding	1
cation binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

902 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ZMYM5	DNAJC12	Q9UKB3	465
ZMYM5	GALNT13	Q8IUC8	452
ZMYM5	RBMS3	Q6XE24	444
ZMYM5	PARD3B	Q8TEW8	440
ZMYM5	RNASEH2B	Q5TBB1	422
ZMYM5	ZNF770	Q6IQ21	384
ZMYM5	PP2D1	A8MPX8	379
ZMYM5	CCDC12	Q8WUD4	377
ZMYM5	C16orf90	A8MZG2	376
ZMYM5	CAMSAP1	Q5T5Y3	376
ZMYM5	PSPC1	Q8WXF1	363
ZMYM5	ZSCAN30	Q86W11	363
ZMYM5	QRICH1	Q2TAL8	357
ZMYM5	ZNF235	Q14590	349
ZMYM5	PTPRD	P23468	344

IntAct

18 interactions, top by confidence:

A	B	Type	Score
SUMO1	ZMYM5	psi-mi:“MI:0915”(physical association)	0.560
ZMYM5	LRRK2	psi-mi:“MI:0407”(direct interaction)	0.440
ZMYM5	DAPK1	psi-mi:“MI:0407”(direct interaction)	0.440
ZMYM5	MFHAS1	psi-mi:“MI:0407”(direct interaction)	0.440
ZMYM5	PCK1	psi-mi:“MI:0915”(physical association)	0.400
ZMYM5	GTF2IRD1	psi-mi:“MI:0915”(physical association)	0.370
ZMYM5		psi-mi:“MI:0915”(physical association)	0.370
ZMYM5	SKIL	psi-mi:“MI:0915”(physical association)	0.370
ZMYM5	SNIP1	psi-mi:“MI:0915”(physical association)	0.370
PRMT1	ZMYM5	psi-mi:“MI:0915”(physical association)	0.370
ITSN1	ZMYM5	psi-mi:“MI:0915”(physical association)	0.000
MORC3	ZMYM5	psi-mi:“MI:0915”(physical association)	0.000
PDE9A	ZMYM5	psi-mi:“MI:0915”(physical association)	0.000
CBS	ZMYM5	psi-mi:“MI:0915”(physical association)	0.000
FTCD	ZMYM5	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (44): ZMYM5 (Two-hybrid), ACAD11 (Affinity Capture-MS), RPS6KA2 (Affinity Capture-MS), RPS6KA3 (Affinity Capture-MS), RPS6KA3 (Affinity Capture-MS), RPS6KA2 (Affinity Capture-MS), ZMYM5 (Two-hybrid), ZMYM5 (Biochemical Activity), ZMYM5 (Reconstituted Complex), ZMYM5 (Reconstituted Complex), ZMYM5 (Reconstituted Complex), ZMYM5 (Two-hybrid), ZMYM5 (Two-hybrid), ZMYM5 (Two-hybrid), ZMYM5 (Two-hybrid)

ESM2 similar proteins: A2VE56, A6QPH9, I3LHS8, O08781, O14545, O54836, P0C6S7, Q14CM0, Q3SZY7, Q3U2E2, Q497H0, Q4R3D6, Q4R970, Q58D05, Q5F3F2, Q5FWF5, Q5R7S6, Q5RDJ2, Q5U2M7, Q5VT97, Q66J85, Q68FE8, Q69Z69, Q6DGF4, Q6FIF0, Q6N043, Q6P2K3, Q70EL2, Q7Z6G8, Q8BIZ1, Q8IWR0, Q8K214, Q8K387, Q8N7W2, Q8N9Z9, Q8NA31, Q8ND82, Q8QFX1, Q91YD3, Q96B23

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	57
Likely benign	6
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1500 predictions. Top by Δscore:

Variant	Effect	Δscore
13:19837669:C:CT	donor_gain	1.0000
13:19837670:T:TC	donor_gain	1.0000
13:19837683:T:TA	donor_gain	1.0000
13:19837692:A:AC	donor_gain	1.0000
13:19837693:T:C	donor_gain	1.0000
13:19837701:T:TA	donor_gain	1.0000
13:19837702:C:CA	donor_gain	1.0000
13:19851346:A:AC	donor_gain	1.0000
13:19851347:C:CC	donor_gain	1.0000
13:19851347:CTG:C	donor_gain	1.0000
13:19862397:A:AC	donor_gain	1.0000
13:19862398:C:CC	donor_gain	1.0000
13:19862398:CA:C	donor_gain	1.0000
13:19862411:T:TA	donor_gain	1.0000
13:19835472:ATTAC:A	donor_loss	0.9900
13:19835473:TTA:T	donor_loss	0.9900
13:19835474:TA:T	donor_loss	0.9900
13:19835475:ACC:A	donor_loss	0.9900
13:19835476:C:A	donor_loss	0.9900
13:19835686:GAATC:G	acceptor_loss	0.9900
13:19835687:AATCT:A	acceptor_loss	0.9900
13:19835689:TC:T	acceptor_loss	0.9900
13:19835690:C:CC	acceptor_gain	0.9900
13:19835690:CTA:C	acceptor_loss	0.9900
13:19835691:T:G	acceptor_loss	0.9900
13:19837681:CAT:C	donor_gain	0.9900
13:19837683:TCTTG:T	donor_gain	0.9900
13:19837686:TG:T	donor_gain	0.9900
13:19837749:A:AC	donor_gain	0.9900
13:19837750:C:CC	donor_gain	0.9900

AlphaMissense

4417 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
13:19824755:A:G	W578R	0.998
13:19824755:A:T	W578R	0.998
13:19838771:A:C	F267L	0.998
13:19838771:A:T	F267L	0.998
13:19838773:A:G	F267L	0.998
13:19835633:G:C	C365W	0.997
13:19835635:A:G	C365R	0.997
13:19838756:G:C	C272W	0.997
13:19838758:A:G	C272R	0.997
13:19838770:A:G	C268R	0.997
13:19838800:A:C	Y258D	0.997
13:19824719:A:G	C590R	0.996
13:19824914:A:G	W525R	0.996
13:19824914:A:T	W525R	0.996
13:19838769:C:G	C268S	0.996
13:19838770:A:T	C268S	0.996
13:19838772:A:G	F267S	0.996
13:19838842:A:G	C244R	0.996
13:19835623:A:C	Y369D	0.995
13:19835634:C:G	C365S	0.995
13:19835635:A:T	C365S	0.995
13:19838768:G:C	C268W	0.995
13:19838802:G:T	A257D	0.995
13:19838840:A:C	C244W	0.995
13:19835604:A:G	L375P	0.994
13:19835618:T:A	R370S	0.994
13:19835618:T:G	R370S	0.994
13:19835630:A:C	F366L	0.994
13:19835630:A:T	F366L	0.994
13:19835631:A:G	F366S	0.994

dbSNP variants (sampled 300 via entrez): RS1000013853 (13:19823002 G>A), RS1000043582 (13:19823206 C>A), RS1000059369 (13:19835394 T>C,G), RS1000109849 (13:19835119 T>C), RS1000195706 (13:19853340 C>T), RS1000301355 (13:19839641 G>A), RS1000579308 (13:19851480 A>G), RS1000600697 (13:19840673 C>A), RS1000675489 (13:19839458 G>A,T), RS1000695538 (13:19853043 G>A,C), RS1000700907 (13:19845703 C>A,T), RS1000762742 (13:19851279 T>C), RS1000795029 (13:19847066 G>C,T), RS1000845426 (13:19829278 T>C), RS1000852138 (13:19863686 GC>G)

Disease associations

OMIM: gene MIM:616443 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
multiple congenital anomalies/dysmorphic syndrome	Limited	Autosomal recessive

Mondo (1): multiple congenital anomalies/dysmorphic syndrome (MONDO:0019042)

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004136_1	Methadone dose in opioid dependence	9.000000e-06
GCST008258_25	Alcohol use disorder (consumption score)	3.000000e-08
GCST010656_1	Arterial stiffness (brachial-ankle pulse wave velocity)	3.000000e-07

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0007907	methadone dose measurement
EFO:0007645	longitudinal alcohol consumption measurement
EFO:0009458	alcohol use disorder measurement
EFO:0004517	arterial stiffness measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

47 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	4
trichostatin A	affects cotreatment, decreases expression	3
Valproic Acid	decreases expression, increases expression	3
Cyclosporine	increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
testosterone enanthate	affects expression	1
methylmercuric chloride	decreases expression	1
alpha-pinene	affects cotreatment, decreases expression, increases abundance	1
pirinixic acid	decreases expression, increases activity, affects binding	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
cobaltous chloride	increases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
methacrylaldehyde	affects cotreatment, decreases expression, increases abundance	1
di-n-butylphosphoric acid	affects expression	1
cylindrospermopsin	increases expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression, affects cotreatment	1
Sunitinib	increases expression	1
Vorinostat	decreases expression	1
Acrolein	affects cotreatment, decreases expression, increases abundance	1
Air Pollutants	affects cotreatment, decreases expression, increases abundance	1
Air Pollutants, Occupational	affects expression	1
Arsenic	increases expression, increases abundance	1
Atrazine	decreases expression	1
Cisplatin	affects cotreatment, decreases expression	1
Coumestrol	decreases expression, affects cotreatment	1
Demecolcine	decreases expression	1

Clinical trials (associated diseases)

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