ZMYM4

zinc finger MYM-type containing 4, the group of Zinc fingers MYM-type

Basic information

Region (hg38): 1:35268709-35422058

Previous symbols: [ "ZNF262" ]

Links

ENSG00000146463 ∙ NCBI:9202 ∙ OMIM:613568 ∙ HGNC:13055 ∙ Uniprot:Q5VZL5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZMYM4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYM4 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						0
missense			46			46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	0	0

Variants in ZMYM4

This is a list of pathogenic ClinVar variants found in the ZMYM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-35269071-G-A		not specified	Uncertain significance (Jun 05, 2023)
1-35359092-G-A		not specified	Uncertain significance (Jan 19, 2024)
1-35359141-T-C		not specified	Uncertain significance (Oct 20, 2023)
1-35359268-T-A		not specified	Uncertain significance (May 13, 2024)
1-35359293-C-T		not specified	Uncertain significance (Feb 14, 2023)
1-35359298-A-T		not specified	Uncertain significance (Apr 28, 2023)
1-35359375-G-A		not specified	Uncertain significance (Sep 20, 2023)
1-35359384-G-A		not specified	Uncertain significance (Mar 08, 2024)
1-35359411-A-G		not specified	Uncertain significance (Oct 26, 2022)
1-35361692-G-T		not specified	Uncertain significance (Aug 10, 2023)
1-35361761-A-G		not specified	Uncertain significance (Sep 29, 2023)
1-35370383-A-G		not specified	Uncertain significance (Oct 05, 2022)
1-35370390-G-T		not specified	Uncertain significance (May 27, 2022)
1-35370473-G-C		not specified	Uncertain significance (Feb 17, 2024)
1-35370482-A-C		not specified	Uncertain significance (Sep 01, 2021)
1-35370593-C-G		not specified	Uncertain significance (Dec 22, 2023)
1-35381296-T-A		not specified	Uncertain significance (Apr 26, 2023)
1-35385452-A-G		not specified	Uncertain significance (Dec 28, 2022)
1-35386082-G-A		not specified	Uncertain significance (Jan 03, 2022)
1-35386152-G-A		not specified	Uncertain significance (Apr 25, 2022)
1-35387063-G-A		not specified	Uncertain significance (Jul 09, 2021)
1-35387133-C-T		not specified	Uncertain significance (Apr 18, 2024)
1-35387168-C-T		not specified	Uncertain significance (Jul 26, 2022)
1-35387241-G-A		not specified	Uncertain significance (Oct 26, 2021)
1-35387243-C-A		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYM4	protein_coding	protein_coding	ENST00000314607	30	153092

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	3.58e-8	125732	0	14	125746	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.86	499	808	0.618	0.0000410	10217
Missense in Polyphen		67	217.34	0.30827		2889
Synonymous	1.65	249	284	0.876	0.0000143	2854
Loss of Function	7.61	8	82.7	0.0968	0.00000448	1033

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000631	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000916	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of cell morphology and cytoskeletal organization. {ECO:0000269|PubMed:21834987}.

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.408
• rvis_EVS: -1.02
• rvis_percentile_EVS: 8.1

Haploinsufficiency Scores

• pHI: 0.736
• hipred: Y
• hipred_score: 0.605
• ghis: 0.672

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.890

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmym4

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cytoskeleton organization;multicellular organism development;regulation of cell morphogenesis
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;zinc ion binding