ZMYM4

gene
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Also known as KIAA0425ZNF198L3MYM

Summary

ZMYM4 (zinc finger MYM-type containing 4, HGNC:13055) is a protein-coding gene on chromosome 1p34.3, encoding Zinc finger MYM-type protein 4 (Q5VZL5). Plays a role in the regulation of cell morphology and cytoskeletal organization.

Predicted to enable DNA binding activity. Involved in cytoskeleton organization and regulation of cell morphogenesis.

Source: NCBI Gene 9202 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 158 total
  • MANE Select transcript: NM_005095

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13055
Approved symbolZMYM4
Namezinc finger MYM-type containing 4
Location1p34.3
Locus typegene with protein product
StatusApproved
AliasesKIAA0425, ZNF198L3, MYM
Ensembl geneENSG00000146463
Ensembl biotypeprotein_coding
OMIM613568
Entrez9202

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000314607, ENST00000441447, ENST00000457946, ENST00000470175, ENST00000482131, ENST00000492456, ENST00000933224, ENST00000933225, ENST00000933226

RefSeq mRNA: 5 — MANE Select: NM_005095 NM_001350138, NM_001350139, NM_001350140, NM_001375653, NM_005095

CCDS: CCDS389

Canonical transcript exons

ENST00000314607 — 30 exons

ExonStartEnd
ENSE000009559383541844335418572
ENSE000010669063540502335405194
ENSE000010669123538544235385592
ENSE000010669143540800835408159
ENSE000010669193538700335387278
ENSE000010669283539737735397545
ENSE000010669293538154635381758
ENSE000010669313541397235414083
ENSE000010669323538994835390098
ENSE000011252293541546635415714
ENSE000011252763539948235399576
ENSE000011252853539886435399043
ENSE000011252943539841335398466
ENSE000011253303539264735392684
ENSE000011253383539221235392352
ENSE000011253523538891035389082
ENSE000011253753538607435386189
ENSE000011254013538125935381433
ENSE000014177673536161935361789
ENSE000014255673536119435361255
ENSE000014291233537037235370627
ENSE000016163883538745435387604
ENSE000016265593541947035422058
ENSE000016707663526870935269085
ENSE000017656193535892535359446
ENSE000034745983539359535393739
ENSE000034780093537002935370113
ENSE000034826543539655235396670
ENSE000036151413532536035325405
ENSE000036882153540537335405468

Expression profiles

Bgee: expression breadth ubiquitous, 299 present calls, max score 96.56.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.4391 / max 204.9543, expressed in 1806 samples.

FANTOM5 promoters (12 alternative TSS)

Promoter IDTPM avgSamples expressed
20879.53581766
20903.09141341
20882.67971356
20941.1860792
20890.8762581
20970.8235512
20960.6809421
21000.4908214
20930.3057128
20950.2778118

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370196.56gold quality
ventricular zoneUBERON:000305395.72gold quality
cortical plateUBERON:000534393.99gold quality
ganglionic eminenceUBERON:000402393.69gold quality
choroid plexus epitheliumUBERON:000391193.34gold quality
cerebellar vermisUBERON:000472093.09gold quality
embryoUBERON:000092292.90gold quality
colonic epitheliumUBERON:000039792.89gold quality
adrenal tissueUBERON:001830392.65gold quality
Brodmann (1909) area 23UBERON:001355492.37gold quality
buccal mucosa cellCL:000233692.24gold quality
cauda epididymisUBERON:000436092.00gold quality
orbitofrontal cortexUBERON:000416791.98gold quality
spermCL:000001991.88gold quality
caput epididymisUBERON:000435891.73gold quality
pigmented layer of retinaUBERON:000178291.71gold quality
male germ cellCL:000001591.57gold quality
germinal epithelium of ovaryUBERON:000130491.39gold quality
middle temporal gyrusUBERON:000277191.30gold quality
epithelial cell of pancreasCL:000008391.17gold quality
Brodmann (1909) area 46UBERON:000648391.12gold quality
diaphragmUBERON:000110390.93silver quality
oviduct epitheliumUBERON:000480490.91gold quality
lateral nuclear group of thalamusUBERON:000273690.58gold quality
parietal pleuraUBERON:000240090.38gold quality
cardiac muscle of right atriumUBERON:000337990.38gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450290.17gold quality
corpus epididymisUBERON:000435990.06gold quality
ponsUBERON:000098890.03gold quality
biceps brachiiUBERON:000150790.02gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes7.50

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

173 targeting ZMYM4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-3646100.0073.565283
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-4510100.0066.602050
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-6127100.0066.762188
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-428299.9975.366408
HSA-MIR-366299.9973.825684
HSA-MIR-150-5P99.9966.691976
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593

Literature-anchored findings (GeneRIF, showing 3)

  • regulates apoptosis by altering mRNA turnover and CDIR inhibits apoptosis by acting as a competitive inhibitor of AUF1, preventing AUF1 from binding to its targets (PMID:12356764)
  • Characterization of the zinc finger proteins ZMYM2 and ZMYM4 as novel B-MYB binding proteins. (PMID:32439918)
  • Expression and Mutation Alterations of ZMYM4 Gene in Gastric and Colonic Cancers. (PMID:33938481)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusZmym4ENSMUSG00000042446
rattus_norvegicusZmym4ENSRNOG00000012397

Paralogs (18): GTF2IRD1 (ENSG00000006704), ZMYM2 (ENSG00000121741), ZMYM5 (ENSG00000132950), THAP12 (ENSG00000137492), 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 4Q5VZL5 (reviewed: Q5VZL5)

Alternative names: Zinc finger protein 262

All UniProt accessions (3): Q5VZL5, A0A0A0MSN3, H7C1I7

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in the regulation of cell morphology and cytoskeletal organization.

Tissue specificity. Expressed at higher level in heart, skeletal muscle, kidney and liver.

Miscellaneous. The 3’-UTR region of the mRNA encoding this protein contains a motif called CDIR (for cell death inhibiting RNA) that binds HNRPD/AUF1 and HSPB1/HSP27. It is able to inhibit interferon-gamma induced apoptosis.

Isoforms (4)

UniProt IDNamesCanonical?
Q5VZL5-11yes
Q5VZL5-22
Q5VZL5-33
Q5VZL5-44

RefSeq proteins (5): NP_001337067, NP_001337068, NP_001337069, NP_001362582, NP_005086* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR010507Znf_MYMDomain
IPR011017TRASH_domDomain
IPR021893ZMYM2-like_CDomain
IPR051284ZnF_MYMT-QRICH1Family
IPR057926QRICH1_domDomain

Pfam: PF06467, PF12012, PF24900, PF25561

UniProt features (58 total): cross-link 20, modified residue 15, zinc finger region 9, region of interest 3, compositionally biased region 3, splice variant 3, sequence variant 2, initiator methionine 1, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5VZL5-F159.700.21

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 (35): 2, 107, 110, 122, 162, 197, 242, 1030, 1064, 1071, 1181, 1256, 1539, 1542, 1547, 140, 149, 195, 201, 232 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 180 (showing top): GOBP_REGULATION_OF_CELL_MORPHOGENESIS, TGCGCANK_UNKNOWN, GCANCTGNY_MYOD_Q6, MORF_HDAC2, CAGCTG_AP4_Q5, CATTTCA_MIR203, MYOD_01, MARTINEZ_RB1_TARGETS_DN, BLALOCK_ALZHEIMERS_DISEASE_UP, HEN1_01, chr1p34, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, GATA1_03, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS, AACTTT_UNKNOWN

GO Biological Process (2): cytoskeleton organization (GO:0007010), regulation of cell morphogenesis (GO:0022604)

GO Molecular Function (4): DNA binding (GO:0003677), 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:

CategoryTerms
organelle organization1
cell morphogenesis1
regulation of anatomical structure morphogenesis1
nucleic acid binding1
transition metal ion binding1
binding1
cation binding1

Protein interactions and networks

STRING

1950 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ZMYM4RCOR1Q9UKL0633
ZMYM4KDM1AO60341498
ZMYM4UFSP2Q9NUQ7489
ZMYM4FGFR1P11362471
ZMYM4FKBP9O95302453
ZMYM4TMEM35BQ8NCS4449
ZMYM4SGSM3Q96HU1443
ZMYM4CHMP7Q8WUX9433
ZMYM4NUBPLQ8TB37431
ZMYM4OTUD3Q5T2D3431
ZMYM4DTYMKP23919420
ZMYM4RNASEH2BQ5TBB1417
ZMYM4ATF7IPQ6VMQ6412
ZMYM4SUMO2P55855394
ZMYM4HDAC1Q13547391
ZMYM4DENND5BQ6ZUT9391

IntAct

190 interactions, top by confidence:

ABTypeScore
CDK8MED19psi-mi:“MI:2364”(proximity)0.850
ZSCAN21ZNF24psi-mi:“MI:0914”(association)0.830
DYNLL1BLTP3Bpsi-mi:“MI:0914”(association)0.730
RHOCRAP1GDS1psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
NFICNFIBpsi-mi:“MI:2364”(proximity)0.690
DYNLL2BLTP3Bpsi-mi:“MI:0914”(association)0.640
QPRTPIK3C2Apsi-mi:“MI:0914”(association)0.640
ZNF397ZNF213psi-mi:“MI:0914”(association)0.640
ZMYM4ROR2psi-mi:“MI:0915”(physical association)0.560
ZMYM4CTCFpsi-mi:“MI:0915”(physical association)0.560
RUNX1T1ZMYM4psi-mi:“MI:0915”(physical association)0.560
ZMYM4FHL2psi-mi:“MI:0915”(physical association)0.560
UBQLN1ZMYM4psi-mi:“MI:0915”(physical association)0.560
ZMYM4UBQLN1psi-mi:“MI:0915”(physical association)0.560
ZMYM4RUNX1T1psi-mi:“MI:0915”(physical association)0.560

BioGRID (224): ZMYM4 (Two-hybrid), ZMYM4 (Two-hybrid), ZMYM4 (Two-hybrid), CTCF (Two-hybrid), UBQLN1 (Two-hybrid), ZMYM4 (Affinity Capture-RNA), ZMYM4 (Affinity Capture-RNA), ZMYM4 (Protein-peptide), ZMYM4 (Affinity Capture-MS), ZMYM4 (Reconstituted Complex), ZMYM4 (Affinity Capture-MS), ZMYM4 (Affinity Capture-MS), ZMYM4 (Affinity Capture-MS), ZMYM4 (Co-fractionation), ZMYM4 (Co-fractionation)

ESM2 similar proteins: A0A1L8GR68, A2A791, B2GUN4, E1BP74, E1BZ85, F1QLG5, F7AQ22, O00472, O15164, O15550, O70546, O88974, O95789, P49140, P55265, P70365, Q14202, Q14596, Q15047, Q15788, Q4PJW2, Q5R413, Q5RC94, Q5RDJ2, Q5VZL5, Q64127, Q69Z66, Q6H8Q1, Q6KC51, Q6NXK2, Q6P3Y5, Q6PFK1, Q7Z3K3, Q8BJ34, Q8BL65, Q8BZH4, Q8CHY6, Q8IZD4, Q8TEW8, Q8VIG2

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.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 232 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane517.4×6e-04
Transport of connexons to the plasma membrane517.4×6e-04
Formation of tubulin folding intermediates by CCT/TriC616.3×3e-04
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding615.7×3e-04
Gap junction trafficking and regulation515.2×7e-04
Gap junction trafficking515.2×7e-04
Post-chaperonin tubulin folding pathway515.2×7e-04
Prefoldin mediated transfer of substrate to CCT/TriC615.2×3e-04

GO biological processes:

GO termPartnersFoldFDR
mRNA processing124.5×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance122
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

5488 predictions. Top by Δscore:

VariantEffectΔscore
1:35269082:GAGG:Gdonor_gain1.0000
1:35269084:GG:Gdonor_gain1.0000
1:35269085:GG:Gdonor_gain1.0000
1:35269085:GGTA:Gdonor_loss1.0000
1:35269086:G:GGdonor_gain1.0000
1:35269087:T:Adonor_loss1.0000
1:35325358:A:AGacceptor_gain1.0000
1:35325359:G:GAacceptor_gain1.0000
1:35325359:GT:Gacceptor_gain1.0000
1:35325359:GTTT:Gacceptor_gain1.0000
1:35325401:GAACT:Gdonor_gain1.0000
1:35325402:AACT:Adonor_gain1.0000
1:35325403:ACT:Adonor_gain1.0000
1:35325404:CT:Cdonor_gain1.0000
1:35325406:G:GGdonor_gain1.0000
1:35358922:AAGGT:Aacceptor_gain1.0000
1:35359119:GATT:Gdonor_gain1.0000
1:35359173:G:GTdonor_gain1.0000
1:35361254:GG:Gdonor_gain1.0000
1:35361255:GG:Gdonor_gain1.0000
1:35361614:TTTA:Tacceptor_loss1.0000
1:35361616:TA:Tacceptor_loss1.0000
1:35361617:A:AGacceptor_gain1.0000
1:35361617:A:Cacceptor_loss1.0000
1:35361617:AG:Aacceptor_gain1.0000
1:35361618:G:GGacceptor_gain1.0000
1:35361618:GG:Gacceptor_gain1.0000
1:35361712:GATGA:Gdonor_gain1.0000
1:35361716:A:Gdonor_gain1.0000
1:35361748:GGAC:Gdonor_gain1.0000

AlphaMissense

10250 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:35370078:T:AI297N1.000
1:35370078:T:CI297T1.000
1:35370078:T:GI297S1.000
1:35370087:T:AV300E1.000
1:35370089:T:CF301L1.000
1:35370091:T:AF301L1.000
1:35370091:T:GF301L1.000
1:35370467:T:AC341S1.000
1:35370467:T:CC341R1.000
1:35370467:T:GC341G1.000
1:35370468:G:AC341Y1.000
1:35370468:G:CC341S1.000
1:35370468:G:TC341F1.000
1:35370469:T:GC341W1.000
1:35370476:T:AC344S1.000
1:35370476:T:CC344R1.000
1:35370477:G:AC344Y1.000
1:35370477:G:CC344S1.000
1:35370477:G:TC344F1.000
1:35370478:T:GC344W1.000
1:35370489:T:AL348H1.000
1:35370489:T:CL348P1.000
1:35370497:G:AG351R1.000
1:35370497:G:CG351R1.000
1:35370498:G:AG351E1.000
1:35370501:A:CQ352P1.000
1:35370507:C:AA354D1.000
1:35370509:T:AY355N1.000
1:35370509:T:CY355H1.000
1:35370509:T:GY355D1.000

dbSNP variants (sampled 300 via entrez): RS1000000642 (1:35269374 G>A), RS1000003586 (1:35417251 AAAAG>A,AAAAGAAAG), RS1000030174 (1:35388550 T>C), RS1000032644 (1:35282589 T>C), RS1000037998 (1:35410791 A>C,G), RS1000044025 (1:35379248 G>A), RS1000058138 (1:35372670 AT>A), RS1000069890 (1:35388181 A>C,G), RS1000100263 (1:35302552 A>G,T), RS1000104423 (1:35294489 G>A,C), RS1000107211 (1:35345484 C>T), RS1000139548 (1:35322131 A>G,T), RS1000162754 (1:35333054 C>T), RS1000172022 (1:35347715 G>A), RS1000175353 (1:35376497 G>A)

Disease associations

OMIM: gene MIM:613568 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST003542_28Night sleep phenotypes8.000000e-08
GCST005038_30Allergic disease (asthma, hay fever or eczema)1.000000e-08
GCST90002394_132Monocyte percentage of white cells2.000000e-13
GCST90020024_12A body shape index5.000000e-08
GCST90020029_1255Waist circumference adjusted for body mass index2.000000e-08

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007989monocyte percentage of leukocytes
EFO:0007789BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression4
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
TAK-243decreases sumoylation1
triphenyl phosphateaffects expression1
geraniolincreases expression1
arseniteaffects binding, decreases reaction1
benzo(e)pyreneincreases methylation1
potassium chromate(VI)decreases expression, affects cotreatment1
aflatoxin B2decreases methylation1
epigallocatechin gallateaffects cotreatment, decreases expression1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
jinfukangaffects cotreatment, decreases expression1
LDN 193189affects cotreatment, increases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Atrazinedecreases expression1
Caffeinedecreases phosphorylation1
Cisplatinaffects cotreatment, decreases expression1
Formaldehydedecreases expression1
Methapyrileneincreases methylation1
Ribonucleotidesaffects binding1
Rotenonedecreases expression1
Seleniumdecreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Aflatoxin M1decreases expression1
Antirheumatic Agentsincreases expression1
Particulate Matterdecreases expression, increases abundance1

Cellosaurus cell lines

4 cell lines: 4 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_1661ZR-75-30Cancer cell lineFemale
CVCL_C7Z8HAP1 ZMYM4 (-) 1Cancer cell lineMale
CVCL_C7Z9HAP1 ZMYM4 (-) 2Cancer cell lineMale
CVCL_C7ZAHAP1 ZMYM4 (-) 3Cancer cell lineMale

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): allergic disease