GeneBe

ZMYM2

zinc finger MYM-type containing 2, the group of Zinc fingers MYM-type

Basic information

Region (hg38): 13:19958677-20091829

Previous symbols: [ "ZNF198" ]

Links

ENSG00000121741 ∙ NCBI:7750 ∙ OMIM:602221 ∙ HGNC:12989 ∙ Uniprot:Q9UBW7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • congenital anomaly of kidney and urinary tract (Strong), mode of inheritance: AD
  • congenital anomaly of kidney and urinary tract (Moderate), mode of inheritance: AD
  • neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities (Strong), mode of inheritance: AD
  • neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities (Strong), mode of inheritance: AD
  • neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalitiesADCardiovascular; RenalAmong other findings, individuals may have congenital cardiovascular and renal anomalies, which may lead to sequelae, and awareness may allow prompt diagnosis and medical or surgical managementCardiovascular; Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Renal32891193

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZMYM2 gene.

  • not_provided (135 variants)
  • Inborn_genetic_diseases (117 variants)
  • Neurodevelopmental-craniofacial_syndrome_with_variable_renal_and_cardiac_abnormalities (57 variants)
  • ZMYM2-related_disorder (30 variants)
  • Congenital_anomaly_of_kidney_and_urinary_tract (15 variants)
  • not_specified (12 variants)
  • Neurodevelopmental_disorder (4 variants)
  • See_cases (3 variants)
  • Combined_oxidative_phosphorylation_deficiency_40 (2 variants)
  • ZMYM2-related_neurodevelopmental_disorder_with_multiple_anomalies (1 variants)
  • Neurodevelopmental_delay (1 variants)
  • Seizure (1 variants)
  • Neurodevelopmental_abnormality (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYM2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000197968.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
10
clinvar
4
clinvar
 15
missense
194
clinvar
7
clinvar
1
clinvar
 202
nonsense
12
clinvar
24
clinvar
3
clinvar
 39
start loss
0
frameshift
26
clinvar
22
clinvar
7
clinvar
 55
splice donor/acceptor (+/-2bp)
1
clinvar
8
clinvar
3
clinvar
 12
Total 39 54 208 17 5

Highest pathogenic variant AF is 0.00008718806

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ZMYM2protein_codingprotein_codingENST00000382869 23133159
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.6660.3341256710251256960.0000995
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.014516710.6720.00003249073
Missense in Polyphen109257.930.42263605
Synonymous1.172112340.9030.00001192483
Loss of Function6.061569.50.2160.00000395895

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002950.000289
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004730.0000462
European (Non-Finnish)0.0001530.000149
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May function as a transcription factor.;
Disease
DISEASE: Note=A chromosomal aberration involving ZMYM2 may be a cause of stem cell leukemia lymphoma syndrome (SCLL). Translocation t(8;13)(p11;q12) with FGFR1. SCLL usually presents as lymphoblastic lymphoma in association with a myeloproliferative disorder, often accompanied by pronounced peripheral eosinophilia and/or prominent eosinophilic infiltrates in the affected bone marrow. {ECO:0000269|PubMed:9716603}.;
Pathway
Disease;Signaling by FGFR in disease;Signaling by cytosolic FGFR1 fusion mutants;FGFR1 mutant receptor activation;Signaling by FGFR1 in disease;Diseases of signal transduction (Consensus)

Recessive Scores

pRec
0.210

Intolerance Scores

loftool
0.773
rvis_EVS
-1.28
rvis_percentile_EVS
5.11

Haploinsufficiency Scores

pHI
0.784
hipred
Y
hipred_score
0.627
ghis
0.661

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.951

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Zmym2
Phenotype
mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process
regulation of transcription by RNA polymerase II;biological_process;peptidyl-tyrosine phosphorylation;regulation of cell morphogenesis
Cellular component
nucleus;cytosol;PML body
Molecular function
DNA-binding transcription factor activity, RNA polymerase II-specific;protein tyrosine kinase activity;protein binding;zinc ion binding;ubiquitin conjugating enzyme binding