ZDHHC17

zinc finger DHHC-type palmitoyltransferase 17, the group of Zinc fingers DHHC-type|Ankyrin repeat domain containing

Basic information

Region (hg38): 12:76764102-76853696

Links

ENSG00000186908 ∙ NCBI:23390 ∙ OMIM:607799 ∙ HGNC:18412 ∙ Uniprot:Q8IUH5 ∙ 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 ZDHHC17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC17 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			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in ZDHHC17

This is a list of pathogenic ClinVar variants found in the ZDHHC17 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-76764252-G-A		not specified	Uncertain significance (May 14, 2024)
12-76764292-A-G		not specified	Uncertain significance (Jan 17, 2024)
12-76764294-A-G		not specified	Uncertain significance (Dec 27, 2022)
12-76805340-G-A		not specified	Uncertain significance (Apr 13, 2023)
12-76809050-A-G		not specified	Uncertain significance (Jan 23, 2023)
12-76809808-C-T		not specified	Uncertain significance (Apr 15, 2024)
12-76809850-A-G		not specified	Uncertain significance (Jun 16, 2023)
12-76809853-G-C		not specified	Uncertain significance (Jun 06, 2023)
12-76815159-T-C		not specified	Uncertain significance (Jun 16, 2024)
12-76822466-C-G		not specified	Uncertain significance (Apr 23, 2024)
12-76822471-G-C		not specified	Uncertain significance (Mar 01, 2024)
12-76822514-A-G		not specified	Uncertain significance (Aug 08, 2022)
12-76827016-G-A		not specified	Uncertain significance (Nov 09, 2021)
12-76828403-C-G		not specified	Uncertain significance (Jun 24, 2022)
12-76828410-T-C		not specified	Uncertain significance (Mar 01, 2023)
12-76842021-A-G		not specified	Uncertain significance (Jan 11, 2023)
12-76846663-T-G		not specified	Uncertain significance (Sep 01, 2021)
12-76848256-A-T		not specified	Uncertain significance (Nov 07, 2022)
12-76848373-A-C		not specified	Uncertain significance (Mar 19, 2024)
12-76848374-T-C		not specified	Uncertain significance (Dec 17, 2021)
12-76849415-G-T		not specified	Uncertain significance (May 03, 2023)
12-76849419-G-A		not specified	Uncertain significance (Jan 27, 2022)
12-76849455-T-C		not specified	Uncertain significance (Jan 29, 2024)
12-76850888-G-A		not specified	Uncertain significance (Nov 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC17	protein_coding	protein_coding	ENST00000426126	17	90109

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000107	124630	0	9	124639	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.57	182	309	0.589	0.0000149	4157
Missense in Polyphen		52	111.7	0.46552		1657
Synonymous	0.829	92	103	0.896	0.00000520	1105
Loss of Function	5.15	2	34.8	0.0575	0.00000170	449

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000158	0.000158
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000481	0.0000464
European (Non-Finnish)	0.0000359	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000351	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Palmitoyltransferase specific for a subset of neuronal proteins, including SNAP25, DLG4/PSD95, GAD2, SYT1 and HTT (PubMed:15603740, PubMed:15489887, PubMed:19139280, PubMed:28757145). Palmitoylates MPP1 in erythrocytes (PubMed:22496366). May be involved in the sorting or targeting of critical proteins involved in the initiating events of endocytosis at the plasma membrane (PubMed:12393793). May play a role in Mg(2+) transport (PubMed:18794299). {ECO:0000269|PubMed:12393793, ECO:0000269|PubMed:15489887, ECO:0000269|PubMed:15603740, ECO:0000269|PubMed:18794299, ECO:0000269|PubMed:19139280, ECO:0000269|PubMed:22496366, ECO:0000269|PubMed:28757145}.
• Pathway: TCR (Consensus)

Recessive Scores

• pRec: 0.203

Intolerance Scores

• loftool: 0.382
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.580
• hipred: Y
• hipred_score: 0.783
• ghis: 0.651

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.814

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc17
• Phenotype: cellular phenotype; growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Zebrafish Information Network

• Gene name: zdhhc17
• Affected structure: motor neuron
• Phenotype tag: abnormal
• Phenotype quality: truncated

Gene ontology

• Biological process: protein palmitoylation;lipoprotein transport;positive regulation of I-kappaB kinase/NF-kappaB signaling;magnesium ion transmembrane transport
• Cellular component: Golgi membrane;Golgi apparatus;integral component of membrane;aggresome;cell junction;cytoplasmic vesicle membrane;Golgi-associated vesicle membrane;presynaptic membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding;magnesium ion transmembrane transporter activity;palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity;identical protein binding