ZMYND8

zinc finger MYND-type containing 8, the group of Zinc fingers MYND-type|PWWP domain containing|Bromodomain containing|PHD finger proteins

Basic information

Region (hg38): 20:47209214-47356889

Previous symbols: [ "PRKCBP1" ]

Links

ENSG00000101040 ∙ NCBI:23613 ∙ OMIM:615713 ∙ HGNC:9397 ∙ Uniprot:Q9ULU4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 62.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_001281775.3	NP_001268704.1	23	yes	-
ENST00000471951.7	ENSP00000420095.2	23	yes	-
NM_012408.6	NP_036540.3	22	-	-
NM_183047.4	NP_898868.1	23	-	-

Phenotypes

GenCC

Source: genCC

• autism spectrum disorder (Limited), mode of inheritance: AD
• neurodevelopmental disorder (Strong), mode of inheritance: AD
• syndromic complex neurodevelopmental disorder (Strong), mode of inheritance: AD
• neurodevelopmental disorder (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZMYND8 gene.

• not_specified (107 variants)
• not_provided (67 variants)
• ZMYND8-related_disorder (6 variants)
• Neurodevelopmental_disorder (4 variants)
• Intellectual_disability (2 variants)
• ZMYND8-associated_neurodevelopmental_disorder (1 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZMYND8 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001281775.3. 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	11	2	17
missense		3	130	13	1	147
nonsense	1		5			6
start loss						0
frameshift	1	1	4			6
splice donor/acceptor (+/-2bp)			8			8
Total	2	4	151	24	3

Highest pathogenic variant AF is 6.841499e-7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZMYND8	protein_coding	protein_coding	ENST00000461685	23	147709

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.04	399	700	0.570	0.0000419	7862
Missense in Polyphen		80	234.01	0.34187		2776
Synonymous	-0.387	294	286	1.03	0.0000204	2207
Loss of Function	6.77	3	59.2	0.0507	0.00000285	719

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000450	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a transcriptional corepressor for KDM5D. Required for KDM5D-mediated down-regulation of diverse metastasis- associated genes; the function seems to involve the recognition of the dual histone signature H3K4me1-H3K14ac. Suppresses prostate cancer cell invasion. {ECO:0000269|PubMed:27477906}.

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.0152
• rvis_EVS: -1.44
• rvis_percentile_EVS: 3.98

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.999

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of transcription, DNA-templated;negative regulation of cell migration;positive regulation of filopodium assembly;positive regulation of dendritic spine development;modulation of excitatory postsynaptic potential;regulation of postsynaptic density protein 95 clustering;positive regulation of dendritic spine maintenance;negative regulation of nucleic acid-templated transcription
• Cellular component: nucleus;cytoplasm;dendritic spine;dendritic shaft
• Molecular function: transcription corepressor activity;protein binding;zinc ion binding;protein domain specific binding;methylated histone binding;protein N-terminus binding;repressing transcription factor binding;lysine-acetylated histone binding