ZMYND19

zinc finger MYND-type containing 19, the group of Zinc fingers MYND-type

Basic information

Region (hg38): 9:137582080-137590512

Links

ENSG00000165724 ∙ NCBI:116225 ∙ OMIM:611424 ∙ HGNC:21146 ∙ Uniprot:Q96E35 ∙ 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 ZMYND19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYND19 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					2	2
missense			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	7	0	2

Variants in ZMYND19

This is a list of pathogenic ClinVar variants found in the ZMYND19 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137582549-C-G		not specified	Uncertain significance (Dec 01, 2022)
9-137582590-G-A		not specified	Uncertain significance (Dec 17, 2023)
9-137583064-G-A			Benign (Dec 31, 2019)
9-137583073-A-G			Benign (Nov 15, 2018)
9-137583101-A-C		not specified	Uncertain significance (Jun 17, 2024)
9-137587013-G-A		not specified	Uncertain significance (Jan 16, 2024)
9-137587039-T-C		not specified	Uncertain significance (Sep 20, 2023)
9-137587055-C-T		not specified	Uncertain significance (Nov 15, 2021)
9-137587096-C-A		not specified	Uncertain significance (Jan 23, 2024)
9-137587103-G-A		not specified	Uncertain significance (Sep 06, 2022)
9-137587733-G-A		not specified	Uncertain significance (Apr 09, 2024)
9-137588722-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYND19	protein_coding	protein_coding	ENST00000298585	6	8412

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.952	0.0482	125705	0	2	125707	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	84	135	0.622	0.00000827	1461
Missense in Polyphen		20	42.99	0.46522		446
Synonymous	-0.118	54	52.9	1.02	0.00000309	429
Loss of Function	3.21	1	13.9	0.0718	7.65e-7	143

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000891	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved as a regulatory molecule in GPR24/MCH-R1 signaling.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.153
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.29

Haploinsufficiency Scores

• pHI: 0.154
• hipred: Y
• hipred_score: 0.662
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zmynd19

Gene ontology

• Cellular component: cytoplasm;plasma membrane;synapse
• Molecular function: protein binding;metal ion binding