ZMYM6

zinc finger MYM-type containing 6, the group of Zinc fingers MYM-type

Basic information

Region (hg38): 1:34986165-35031945

Previous symbols: [ "ZNF258" ]

Links

ENSG00000163867 ∙ NCBI:9204 ∙ OMIM:613567 ∙ HGNC:13050 ∙ Uniprot:O95789 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal dominant 40 (Limited), mode of inheritance: AD
• intellectual disability (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZMYM6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYM6 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				4	3	7
missense			47	6	6	59
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	3	5
non coding					2	2
Total	0	0	47	10	11

Variants in ZMYM6

This is a list of pathogenic ClinVar variants found in the ZMYM6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-34987101-T-C		ZMYM6-related disorder	Benign (Feb 28, 2019)
1-34987168-G-A		not specified	Uncertain significance (Nov 07, 2022)
1-34987237-T-C		not specified	Uncertain significance (Jul 13, 2022)
1-34987268-T-C		not specified	Uncertain significance (Feb 15, 2023)
1-34987385-C-T		ZMYM6-related disorder	Benign (Apr 11, 2019)
1-34987456-C-T		not specified	Uncertain significance (Nov 10, 2022)
1-34987490-A-C		not specified	Uncertain significance (Jun 23, 2021)
1-34987589-T-C		not specified	Uncertain significance (May 26, 2023)
1-34987613-G-A		not specified	Uncertain significance (May 07, 2024)
1-34987684-G-A		not specified	Uncertain significance (Nov 16, 2021)
1-34987764-A-G		ZMYM6-related disorder	Likely benign (May 08, 2019)
1-34987795-T-C		not specified	Uncertain significance (Apr 12, 2022)
1-34988017-A-G		ZMYM6-related disorder	Likely benign (May 23, 2022)
1-34988050-A-C		ZMYM6-related disorder	Benign (Feb 20, 2019)
1-34988070-T-C		ZMYM6-related disorder	Likely benign (May 31, 2019)
1-34988170-T-G		ZMYM6-related disorder	Likely benign (Mar 05, 2019)
1-34988276-G-A		ZMYM6-related disorder	Benign (May 16, 2019)
1-34988277-A-G		ZMYM6-related disorder	Benign (Jul 31, 2018)
1-34988514-A-G		ZMYM6-related disorder	Benign (Oct 29, 2019)
1-34988645-A-G		not specified	Uncertain significance (Apr 10, 2023)
1-34988717-A-G			Likely benign (Jun 06, 2018)
1-34988770-C-T		not specified	Uncertain significance (Nov 09, 2023)
1-34988872-C-G		ZMYM6-related disorder	Benign (Jun 21, 2019)
1-34988906-C-T		not specified	Uncertain significance (Jan 23, 2024)
1-34992240-G-C		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYM6	protein_coding	protein_coding	ENST00000357182	15	48047

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.27e-13	1.00	125695	0	53	125748	0.000211

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	529	651	0.812	0.0000315	8693
Missense in Polyphen		112	177.7	0.63028		2476
Synonymous	2.02	191	230	0.831	0.0000111	2461
Loss of Function	3.47	30	58.7	0.511	0.00000317	821

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000178
Ashkenazi Jewish	0.00	0.00
East Asian	0.000353	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000267	0.000264
Middle Eastern	0.000353	0.000326
South Asian	0.000264	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0906

Intolerance Scores

• loftool: 0.946
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.9

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.273
• ghis: 0.595

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.756

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmym6

Gene ontology

• Biological process: cytoskeleton organization;multicellular organism development;regulation of cell morphogenesis
• Cellular component: nucleus
• Molecular function: DNA binding;zinc ion binding