ZMYND19

protein-coding

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

Gene summary

ZMYND19 is a MYND zinc finger domain-containing protein that binds to the C terminus of melanin-concentrating hormone receptor-1 (MCHR1; MIM 601751) (Bachner et al., 2002 [PubMed 12208518]), and to the N termini of alpha-tubulin (TUBA1; MIM 191110), and beta-tubulin (TUBB; MIM 191130) (Francke et al., 2005 [PubMed 16039987]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_138462.3

Inheritance

—

ClinVar variants

U:27B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr9:137,582,081-137,590,512

External References & Databases

Ensembl (ENSG00000165724)

Transcript & Mutation Effects

hg38 • Region Span ~8.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ZMYND19 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 24

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_138462.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			26 clinvar			26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	27	0	2	29

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_138462.3	RefSeq	NP_612471.1	6	MANE Select
ENST00000298585.3	Ensembl	ENSP00000298585.2	6	MANE Select
ENST00000923514.1	Ensembl	ENSP00000593573.1	7	Standard
ENST00000923514.2	Ensembl	ENSP00000593573.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
metal ion binding

Cellular Component

cytoplasm
plasma membrane
synapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298585
Coding exons: 6
Length: 8412
Individuals with no LoFs: 125705
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125707
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.56	84	135	0.622	0.00000827	1461
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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