ZDHHC5

zinc finger DHHC-type palmitoyltransferase 5, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 11:57667747-57701182

Links

ENSG00000156599 ∙ NCBI:25921 ∙ OMIM:614586 ∙ HGNC:18472 ∙ Uniprot:Q9C0B5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZDHHC5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC5 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				1		1
missense			54			54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	1	0

Variants in ZDHHC5

This is a list of pathogenic ClinVar variants found in the ZDHHC5 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57673119-A-C		not specified	Uncertain significance (Mar 07, 2024)
11-57673133-G-A		not specified	Uncertain significance (May 30, 2022)
11-57673174-G-A			Likely benign (Jun 13, 2018)
11-57682450-C-G		not specified	Uncertain significance (Aug 12, 2021)
11-57682472-C-T		not specified	Uncertain significance (Jun 02, 2024)
11-57682499-A-G		not specified	Uncertain significance (Sep 06, 2022)
11-57682519-A-G		not specified	Uncertain significance (Dec 11, 2024)
11-57688589-T-C		not specified	Uncertain significance (Sep 26, 2023)
11-57688609-C-T		not specified	Uncertain significance (Feb 27, 2024)
11-57690033-A-C		not specified	Uncertain significance (Mar 01, 2025)
11-57690187-G-A		not specified	Uncertain significance (Jan 22, 2025)
11-57690191-G-A		not specified	Uncertain significance (Nov 10, 2024)
11-57690382-G-A		not specified	Uncertain significance (Dec 06, 2023)
11-57690388-C-T		not specified	Uncertain significance (Mar 11, 2025)
11-57692630-G-A		not specified	Uncertain significance (Jan 16, 2024)
11-57692675-G-A		not specified	Uncertain significance (Jan 23, 2025)
11-57693785-A-G		not specified	Uncertain significance (Aug 28, 2024)
11-57693851-C-T		not specified	Uncertain significance (May 12, 2024)
11-57693866-C-G		not specified	Uncertain significance (Dec 19, 2022)
11-57693894-G-C		not specified	Uncertain significance (Dec 27, 2022)
11-57695947-A-G		not specified	Uncertain significance (Jan 24, 2024)
11-57695957-C-T		not specified	Uncertain significance (Sep 22, 2023)
11-57696791-C-T		not specified	Uncertain significance (Nov 03, 2023)
11-57696800-C-T		not specified	Uncertain significance (Oct 07, 2024)
11-57696803-T-C		not specified	Uncertain significance (Dec 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC5	protein_coding	protein_coding	ENST00000287169	11	33441

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000560	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	329	438	0.751	0.0000266	4573
Missense in Polyphen		80	133.17	0.60075		1454
Synonymous	0.0191	162	162	0.998	0.00000887	1523
Loss of Function	5.39	0	33.9	0.00	0.00000225	368

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000352
Middle Eastern	0.000112	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Palmitoyl acyltransferase for the G-protein coupled receptor SSTR5. Also palmitoylates FLOT2 (By similarity). {ECO:0000250, ECO:0000269|PubMed:21820437}.
• Pathway: EGFR1 (Consensus)

Intolerance Scores

• loftool: 0.0405
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.82

Haploinsufficiency Scores

• pHI: 0.545
• hipred: Y
• hipred_score: 0.768
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.534

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc5

Gene ontology

• Biological process: protein palmitoylation
• Cellular component: plasma membrane;membrane;integral component of membrane;dendrite
• Molecular function: palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity