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

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities	AD	Cardiovascular; Renal	Among 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 management	Cardiovascular; Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Renal	32891193

ClinVar

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

• not provided (9 variants)
• Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities (7 variants)
• Inborn genetic diseases (6 variants)
• Neurodevelopmental disorder (1 variants)
• Congenital anomaly of kidney and urinary tract (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	10	4	15
missense			94	4	1	99
nonsense	9	11	1			21
start loss						0
frameshift	14	9	3			26
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	1	2			4
splice region		1	3	1		5
non coding				1	2	3
Total	24	21	102	15	7

Variants in ZMYM2

This is a list of pathogenic ClinVar variants found in the ZMYM2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-19993066-C-T		ZMYM2-related disorder	Likely benign (Apr 01, 2019)
13-19993089-T-C		ZMYM2-related disorder	Uncertain significance (Aug 15, 2024)
13-19993112-C-G			Uncertain significance (Dec 07, 2023)
13-19993113-A-C		Inborn genetic diseases	Uncertain significance (Mar 14, 2023)
13-19993118-C-A		ZMYM2-related disorder	Uncertain significance (Jun 02, 2023)
13-19993187-G-A		Inborn genetic diseases	Uncertain significance (May 09, 2023)
13-19993212-A-G		Inborn genetic diseases	Uncertain significance (Jan 05, 2022)
13-19993227-C-T		Inborn genetic diseases	Uncertain significance (Dec 14, 2022)
13-19993304-G-A		Inborn genetic diseases	Uncertain significance (May 23, 2024)
13-19993316-A-G		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
13-19993335-A-G			Uncertain significance (Jan 03, 2024)
13-19993345-A-T			Uncertain significance (Oct 09, 2022)
13-19993346-C-CTACA		Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities	Uncertain significance (Jul 13, 2022)
13-19993348-A-G		ZMYM2-related disorder	Benign (Jul 06, 2018)
13-19993361-T-G		not specified	Uncertain significance (Aug 14, 2023)
13-19993404-G-A			Uncertain significance (Jun 17, 2022)
13-19993408-TG-T		Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities	Likely pathogenic (Sep 29, 2022)
13-19993441-G-A		ZMYM2-related disorder	Likely benign (Sep 13, 2019)
13-19993443-A-T			Uncertain significance (Oct 06, 2022)
13-19993463-C-T		Inborn genetic diseases	Pathogenic (Feb 02, 2021)
13-19993493-C-T		ZMYM2-related disorder	Uncertain significance (Nov 22, 2023)
13-19993509-C-G		Inborn genetic diseases	Uncertain significance (Feb 27, 2024)
13-19993526-G-C		Neurodevelopmental-craniofacial syndrome with variable renal and cardiac abnormalities	Benign/Likely benign (Jan 01, 2024)
13-19993641-T-G		Inborn genetic diseases	Pathogenic (Sep 15, 2021)
13-19993694-C-T		Congenital anomaly of kidney and urinary tract	Likely pathogenic (Sep 04, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYM2	protein_coding	protein_coding	ENST00000382869	23	133159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.666	0.334	125671	0	25	125696	0.0000995

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.01	451	671	0.672	0.0000324	9073
Missense in Polyphen		109	257.93	0.4226		3605
Synonymous	1.17	211	234	0.903	0.0000119	2483
Loss of Function	6.06	15	69.5	0.216	0.00000395	895

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000295	0.000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000473	0.0000462
European (Non-Finnish)	0.000153	0.000149
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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