ZMYND12

zinc finger MYND-type containing 12, the group of Zinc fingers MYND-type

Basic information

Region (hg38): 1:42430329-42456253

Links

ENSG00000066185 ∙ NCBI:84217 ∙ ∙ HGNC:21192 ∙ Uniprot:Q9H0C1 ∙ 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 ZMYND12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYND12 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				3	1	4
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	5	1

Variants in ZMYND12

This is a list of pathogenic ClinVar variants found in the ZMYND12 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-42433155-C-A		not specified	Uncertain significance (Mar 23, 2023)
1-42433165-T-G		not specified	Uncertain significance (Oct 29, 2021)
1-42433178-C-A		not specified	Uncertain significance (Dec 13, 2021)
1-42433199-T-C		not specified	Likely benign (Nov 21, 2024)
1-42433201-G-T		not specified	Uncertain significance (Jul 13, 2021)
1-42436474-T-C		not specified	Uncertain significance (Oct 29, 2024)
1-42436525-C-T		not specified	Uncertain significance (Jun 22, 2023)
1-42436530-C-G		not specified	Uncertain significance (Nov 25, 2024)
1-42439876-G-A		not specified	Uncertain significance (Aug 17, 2021)
1-42439884-T-C		not specified	Uncertain significance (Sep 09, 2024)
1-42439901-T-C		not specified	Likely benign (Oct 01, 2024)
1-42439923-C-T		not specified	Uncertain significance (May 06, 2022)
1-42439948-T-C		not specified	Uncertain significance (Dec 30, 2024)
1-42439950-C-T		not specified	Uncertain significance (Nov 09, 2021)
1-42439954-A-C		not specified	Uncertain significance (Jul 12, 2022)
1-42439984-C-T		not specified	Uncertain significance (Aug 12, 2024)
1-42439990-A-T		not specified	Uncertain significance (Feb 13, 2024)
1-42440020-C-A		not specified	Uncertain significance (Jun 12, 2023)
1-42448511-A-G		not specified	Uncertain significance (Mar 20, 2023)
1-42448544-C-T		not specified	Uncertain significance (Jan 19, 2022)
1-42448545-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-42448634-T-C		not specified	Uncertain significance (Jun 25, 2024)
1-42449921-C-T		not specified	Likely benign (Dec 18, 2023)
1-42449936-C-T		not specified	Likely benign (Jul 14, 2024)
1-42449952-C-T		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYND12	protein_coding	protein_coding	ENST00000372565	8	25939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000408	0.960	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.706	172	200	0.860	0.0000106	2366
Missense in Polyphen		35	42.797	0.81782		462
Synonymous	0.848	67	76.4	0.877	0.00000379	702
Loss of Function	1.87	10	18.7	0.534	9.40e-7	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000218	0.000217
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000470	0.0000462
European (Non-Finnish)	0.000188	0.000176
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.000350	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.640
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.38

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.322
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0966

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmynd12

Gene ontology

• Molecular function: metal ion binding