ZDHHC15

zinc finger DHHC-type palmitoyltransferase 15, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): X:75368427-75523502

Links

ENSG00000102383

∙ NCBI:158866 ∙ OMIM:300576 ∙ HGNC:20342 ∙ Uniprot:Q96MV8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

intellectual disability, X-linked 91 (Limited), mode of inheritance: XL
intellectual disability, X-linked 91 (Limited), mode of inheritance: Unknown
X-linked complex neurodevelopmental disorder (Disputed Evidence), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mental retardation, X-linked 91	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	15915161

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZDHHC15 gene.

not_specified (32 variants)
not_provided (16 variants)
Spastic_diplegia (1 variants)
ZDHHC15-related_condition (1 variants)
Oculocutaneous_albinism_type_1B (1 variants)
Intellectual_disability,_X-linked_91 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC15 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000144969.3. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar	1 clinvar	5
missense		1 clinvar	28 clinvar	5 clinvar		34
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	32	6	1

Highest pathogenic variant AF is 0.000005795604

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC15	protein_coding	protein_coding	ENST00000373367	11	155076

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.840	0.160	120673	0	2	120675	0.00000829

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	87	118	0.735	0.00000837	2225
Missense in Polyphen		12	31.695	0.37861		598
Synonymous	-0.0399	43	42.7	1.01	0.00000304	605
Loss of Function	3.08	2	14.8	0.135	0.00000101	262

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000255	0.0000182
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes palmitoylation of Cys residues on target proteins. Catalyzes palmitoylation of GAP43 and DLG4/PSD95. {ECO:0000250|UniProtKB:Q8BGJ0}.;
Disease: DISEASE: Mental retardation, X-linked 91 (MRX91) [MIM:300577]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Intellectual deficiency is the only primary symptom of non- syndromic X-linked mental retardation, while syndromic mental retardation presents with associated physical, neurological and/or psychiatric manifestations. {ECO:0000269|PubMed:15915161}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.0931

Intolerance Scores

loftool: 0.178
rvis_EVS: -0.05
rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

pHI: 0.238
hipred: Y
hipred_score: 0.630
ghis: 0.554

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.208

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Zdhhc15
Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype; growth/size/body region phenotype;

Zebrafish Information Network

Gene name: zdhhc15b
Affected structure: forebrain
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: protein targeting to membrane;synaptic vesicle maturation;peptidyl-L-cysteine S-palmitoylation;protein palmitoylation
Cellular component: Golgi membrane;endoplasmic reticulum;Golgi apparatus;integral component of membrane
Molecular function: palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity;metal ion binding