ZDHHC6

zinc finger DHHC-type palmitoyltransferase 6, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 10:112424427-112447572

Links

ENSG00000023041 ∙ NCBI:64429 ∙ OMIM:618715 ∙ HGNC:19160 ∙ Uniprot:Q9H6R6 ∙ 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 ZDHHC6 gene.

• Inborn genetic diseases (12 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC6 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	3
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	3

Variants in ZDHHC6

This is a list of pathogenic ClinVar variants found in the ZDHHC6 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-112425357-T-C		not specified	Uncertain significance (Jun 18, 2021)
10-112425417-T-C		not specified	Uncertain significance (Dec 14, 2023)
10-112425473-A-C		not specified	Uncertain significance (Dec 21, 2022)
10-112425479-C-T		not specified	Uncertain significance (Dec 17, 2023)
10-112426304-C-T		not specified	Uncertain significance (Dec 19, 2022)
10-112426334-C-T		not specified	Uncertain significance (Mar 24, 2023)
10-112427278-A-C		not specified	Uncertain significance (Oct 17, 2023)
10-112430826-T-C		not specified	Uncertain significance (Dec 06, 2022)
10-112430856-G-T		not specified	Uncertain significance (Apr 07, 2023)
10-112430886-C-G		not specified	Uncertain significance (Apr 28, 2023)
10-112438345-A-G			Benign (Dec 04, 2017)
10-112438359-T-C		not specified	Uncertain significance (Sep 28, 2022)
10-112440581-A-G			Benign (May 21, 2018)
10-112440609-T-C			Benign (May 21, 2018)
10-112440668-T-C		not specified	Uncertain significance (Jan 24, 2023)
10-112442193-C-T		not specified	Uncertain significance (Jan 04, 2024)
10-112442218-T-C		not specified	Uncertain significance (Dec 17, 2023)
10-112442278-T-G		not specified	Uncertain significance (Jun 06, 2023)
10-112442283-G-A		not specified	Uncertain significance (Apr 08, 2022)
10-112443543-G-T		not specified	Uncertain significance (Jan 17, 2024)
10-112445216-T-C		not specified	Uncertain significance (Nov 09, 2021)
10-112445228-T-G		not specified	Uncertain significance (Oct 13, 2023)
10-112445271-C-A		not specified	Uncertain significance (Jul 12, 2022)
10-112445300-T-C		not specified	Uncertain significance (Jun 05, 2023)
10-112445409-A-G		not specified	Uncertain significance (Jun 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC6	protein_coding	protein_coding	ENST00000369405	10	16615

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000160	0.993	125708	0	33	125741	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.707	191	221	0.866	0.0000109	2730
Missense in Polyphen		44	53.637	0.82034		659
Synonymous	1.29	57	70.8	0.805	0.00000354	726
Loss of Function	2.40	12	25.0	0.481	0.00000128	301

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000878	0.0000878
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000327	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000187	0.000176
Middle Eastern	0.000327	0.000326
South Asian	0.000113	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Endoplasmic reticulum palmitoyl acyltransferase that mediates palmitoylation of proteins such as AMFR, CALX, ITPR1 and TFRC (PubMed:22314232, PubMed:22728137, PubMed:25368151, PubMed:28826475). Palmitoylates calnexin (CALX), which is required for its association with the ribosome-translocon complex and efficient folding of glycosylated proteins (PubMed:22314232). Mediates palmitoylation of AMFR, promoting AMFR distribution to the peripheral endoplasmic reticulum (PubMed:22728137). Together with SELENOK, palmitoylates ITPR1 in immune cells, leading to regulate ITPR1 stability and function (PubMed:25368151). {ECO:0000269|PubMed:22314232, ECO:0000269|PubMed:22728137, ECO:0000269|PubMed:25368151, ECO:0000269|PubMed:28826475}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.829
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.09

Haploinsufficiency Scores

• pHI: 0.377
• hipred: N
• hipred_score: 0.398
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.343

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc6

Gene ontology

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