ZDHHC3

zinc finger DHHC-type palmitoyltransferase 3, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 3:44915256-44976185

Links

ENSG00000163812 ∙ NCBI:51304 ∙ OMIM:617150 ∙ HGNC:18470 ∙ Uniprot:Q9NYG2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZDHHC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC3 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	10	1	0

Variants in ZDHHC3

This is a list of pathogenic ClinVar variants found in the ZDHHC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-44929365-G-A		not specified	Uncertain significance (Jan 16, 2024)
3-44929430-C-G			not provided (-)
3-44945201-C-T		not specified	Uncertain significance (Dec 07, 2023)
3-44945253-C-T		not specified	Uncertain significance (Jan 31, 2022)
3-44958627-C-T			Likely benign (Apr 10, 2018)
3-44959150-C-T		not specified	Uncertain significance (Jan 09, 2023)
3-44959196-T-C		not specified	Uncertain significance (Jul 20, 2021)
3-44959217-C-T		not specified	Uncertain significance (Dec 27, 2023)
3-44959225-C-T		not specified	Uncertain significance (Aug 17, 2022)
3-44959290-G-A			not provided (-)
3-44959301-C-T		not specified	Uncertain significance (Dec 20, 2022)
3-44959351-T-C		not specified	Uncertain significance (Nov 07, 2022)
3-44959354-G-C		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC3	protein_coding	protein_coding	ENST00000296127	7	60929

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0277	0.970	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	112	193	0.580	0.0000109	2170
Missense in Polyphen		26	64.005	0.40622		757
Synonymous	0.494	68	73.4	0.927	0.00000465	609
Loss of Function	2.69	6	18.5	0.324	0.00000112	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000704	0.0000703
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Palmitoyltransferase with broad specificity (PubMed:21926431, PubMed:23034182). Palmitoylates GABA receptors on their gamma subunit (GABRG1, GABRG2 and GABRG3), which regulates synaptic clustering and/or cell surface stability (By similarity). Palmitoylates glutamate receptors GRIA1 and GRIA2, which leads to their retention in Golgi. May also palmitoylate DLG4, DNAJC5 and SNAP25 (By similarity). {ECO:0000250|UniProtKB:Q8R173, ECO:0000269|PubMed:21926431, ECO:0000269|PubMed:23034182}.

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.708
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.280
• hipred: Y
• hipred_score: 0.627
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.692

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc3

Gene ontology

• Biological process: protein targeting to membrane;peptidyl-L-cysteine S-palmitoylation;protein palmitoylation;localization within membrane;protein localization to photoreceptor outer segment
• Cellular component: Golgi membrane;endoplasmic reticulum;Golgi apparatus;membrane;integral component of membrane
• Molecular function: palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity