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 (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.

• not_specified (114 variants)
• ZMYM6-related_disorder (20 variants)
• not_provided (3 variants)

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. These statistics are base on transcript: NM_000007167.4. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	3	7
missense			114	8	6	128
nonsense			1			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	117	12	9

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