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: XLD
• 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.

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.

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	1	5
missense			18	3		21
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2	1	2	5
non coding						0
Total	0	0	22	4	1

Variants in ZDHHC15

This is a list of pathogenic ClinVar variants found in the ZDHHC15 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-75379158-T-C		not specified	Benign/Likely benign (Jan 01, 2024)
X-75379162-G-A		not specified	Uncertain significance (Feb 27, 2024)
X-75379174-A-G		not specified	Conflicting classifications of pathogenicity (Nov 01, 2022)
X-75417103-G-A			Uncertain significance (Jun 23, 2015)
X-75417147-A-T		not specified	Uncertain significance (Oct 04, 2022)
X-75421874-T-C		not specified	Uncertain significance (Nov 03, 2022)
X-75421896-C-G		not specified	Benign/Likely benign (Mar 01, 2022)
X-75421973-C-T			Uncertain significance (Jun 21, 2024)
X-75421979-T-A		not specified	Uncertain significance (Jun 26, 2023)
X-75421980-G-A		not specified	Benign (Aug 05, 2019)
X-75424721-A-G			Uncertain significance (Jan 01, 2024)
X-75424755-G-T		not specified	Uncertain significance (Nov 03, 2022)
X-75424765-C-A		not specified	Uncertain significance (Aug 17, 2017)
X-75429082-C-T		Intellectual disability, X-linked 91	Uncertain significance (Feb 21, 2018)
X-75429100-C-T		not specified	Conflicting classifications of pathogenicity (Nov 01, 2022)
X-75429115-G-C		not specified	Uncertain significance (Feb 27, 2024)
X-75429195-A-C			Uncertain significance (Oct 01, 2018)
X-75429957-T-C		Spastic diplegia	Likely pathogenic (-)
X-75429984-C-T		not specified	Likely benign (May 05, 2016)
X-75431452-T-C		Oculocutaneous albinism type 1B	Uncertain significance (May 08, 2023)
X-75431455-C-A		not specified	Uncertain significance (Mar 21, 2023)
X-75431463-G-T			Uncertain significance (Dec 01, 2022)
X-75431511-A-T			Likely benign (Jun 12, 2017)
X-75431515-G-C			Uncertain significance (Oct 01, 2018)
X-75431518-C-G		not specified	Uncertain significance (Jul 09, 2021)

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