ZDHHC1

zinc finger DHHC-type containing 1, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 16:67394152-67416833

Previous symbols: [ "C16orf1" ]

Links

ENSG00000159714 ∙ NCBI:29800 ∙ ∙ HGNC:17916 ∙ Uniprot:Q8WTX9 ∙ 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 ZDHHC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC1 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	2
missense			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	2	1

Variants in ZDHHC1

This is a list of pathogenic ClinVar variants found in the ZDHHC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67394695-C-A		not specified	Likely benign (May 30, 2024)
16-67394704-G-A		not specified	Uncertain significance (May 01, 2022)
16-67394712-T-A		not specified	Uncertain significance (Aug 10, 2023)
16-67394713-C-T		not specified	Uncertain significance (Jun 01, 2023)
16-67394722-C-G		not specified	Uncertain significance (Mar 04, 2024)
16-67394733-G-A		not specified	Uncertain significance (Jan 16, 2024)
16-67394863-G-A		not specified	Uncertain significance (Dec 05, 2022)
16-67394890-G-C		not specified	Uncertain significance (Jun 07, 2023)
16-67394893-C-T		not specified	Uncertain significance (Aug 08, 2022)
16-67395010-G-A		not specified	Uncertain significance (Dec 16, 2023)
16-67395018-G-A		not specified	Uncertain significance (Dec 16, 2023)
16-67395019-G-A		not specified	Uncertain significance (May 27, 2022)
16-67395075-G-A		not specified	Likely benign (Aug 16, 2021)
16-67395111-A-G		not specified	Uncertain significance (Aug 16, 2021)
16-67395135-T-G		not specified	Uncertain significance (Feb 16, 2023)
16-67395154-C-T		not specified	Uncertain significance (Apr 22, 2022)
16-67395184-T-A		not specified	Uncertain significance (Oct 10, 2023)
16-67395487-G-A		not specified	Uncertain significance (Oct 10, 2023)
16-67395506-C-G		not specified	Likely benign (Jun 05, 2024)
16-67398222-C-T		not specified	Uncertain significance (Feb 15, 2023)
16-67398264-T-G		not specified	Uncertain significance (Apr 08, 2024)
16-67398269-C-A		not specified	Uncertain significance (Dec 13, 2023)
16-67398276-G-T		not specified	Uncertain significance (Apr 07, 2023)
16-67398282-C-T		not specified	Uncertain significance (Mar 21, 2023)
16-67398612-C-T		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC1	protein_coding	protein_coding	ENST00000348579	10	22415

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.84e-10	0.368	125710	0	35	125745	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	247	303	0.816	0.0000201	3068
Missense in Polyphen		38	54.531	0.69685		627
Synonymous	0.132	127	129	0.985	0.00000898	1026
Loss of Function	0.958	17	21.8	0.779	0.00000111	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000454	0.000453
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000490	0.000489
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.741
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.56

Haploinsufficiency Scores

• pHI: 0.0831
• hipred: N
• hipred_score: 0.208
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.440

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc1

Gene ontology

• Biological process: protein targeting to membrane;peptidyl-L-cysteine S-palmitoylation;protein palmitoylation
• Cellular component: endoplasmic reticulum;Golgi apparatus;integral component of membrane;extracellular exosome
• Molecular function: DNA binding;palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity