ZMYM1

zinc finger MYM-type containing 1, the group of Zinc fingers MYM-type

Basic information

Region (hg38): 1:35032172-35118818

Links

ENSG00000197056 ∙ NCBI:79830 ∙ ∙ HGNC:26253 ∙ Uniprot:Q5SVZ6 ∙ 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 ZMYM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYM1 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			61	5		66
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	61	5	0

Variants in ZMYM1

This is a list of pathogenic ClinVar variants found in the ZMYM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-35094043-G-A		not specified	Uncertain significance (Oct 03, 2024)
1-35094072-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-35095873-G-A		not specified	Likely benign (Jul 05, 2024)
1-35097391-A-G		not specified	Uncertain significance (Jan 30, 2024)
1-35097452-C-G		not specified	Uncertain significance (Oct 17, 2024)
1-35104341-A-G		not specified	Uncertain significance (May 27, 2022)
1-35104416-A-G		not specified	Uncertain significance (Jan 02, 2024)
1-35104436-G-C		not specified	Uncertain significance (Nov 24, 2024)
1-35104603-G-A		not specified	Uncertain significance (Mar 11, 2022)
1-35104647-A-G		not specified	Uncertain significance (Dec 28, 2023)
1-35104668-G-A		not specified	Uncertain significance (Jul 31, 2024)
1-35104701-C-G		not specified	Uncertain significance (Oct 26, 2022)
1-35110296-A-T		not specified	Uncertain significance (Oct 06, 2022)
1-35110363-A-T		not specified	Uncertain significance (Oct 06, 2021)
1-35110364-C-T		not specified	Uncertain significance (Jan 08, 2024)
1-35110384-G-C		not specified	Uncertain significance (Apr 10, 2023)
1-35111804-A-G		not specified	Uncertain significance (Oct 12, 2022)
1-35111819-C-A		not specified	Uncertain significance (Aug 30, 2024)
1-35111834-A-G		not specified	Uncertain significance (Aug 28, 2024)
1-35111873-G-A		not specified	Uncertain significance (May 31, 2023)
1-35111893-G-A		not specified	Uncertain significance (May 07, 2024)
1-35111907-T-C		not specified	Uncertain significance (Jul 12, 2023)
1-35112113-G-A		not specified	Uncertain significance (Apr 26, 2023)
1-35113043-G-A		not specified	Uncertain significance (Nov 01, 2021)
1-35113066-C-G		not specified	Likely benign (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYM1	protein_coding	protein_coding	ENST00000373330	9	56074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.32e-8	1.00	125125	0	48	125173	0.000192

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.50	460	560	0.821	0.0000260	7557
Missense in Polyphen		95	158.5	0.59937		2338
Synonymous	0.609	192	203	0.946	0.0000102	2068
Loss of Function	3.38	21	45.6	0.460	0.00000237	658

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000466	0.000461
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000218
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000171	0.000167
Middle Eastern	0.000223	0.000218
South Asian	0.000370	0.000359
Other	0.000335	0.000329

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0914

Intolerance Scores

• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.3

Haploinsufficiency Scores

• pHI: 0.0578
• hipred: N
• hipred_score: 0.270
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.204

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmym1

Gene ontology

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