ZDHHC20

zinc finger DHHC-type palmitoyltransferase 20, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 13:21348784-21459370

Links

ENSG00000180776 ∙ NCBI:253832 ∙ OMIM:617972 ∙ HGNC:20749 ∙ Uniprot:Q5W0Z9 ∙ 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 ZDHHC20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC20 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	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	19	1	0

Variants in ZDHHC20

This is a list of pathogenic ClinVar variants found in the ZDHHC20 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-21376655-C-T		not specified	Uncertain significance (Jun 13, 2023)
13-21381463-T-C		not specified	Uncertain significance (Feb 14, 2024)
13-21381532-G-C		not specified	Uncertain significance (Feb 01, 2023)
13-21381545-C-G		not specified	Uncertain significance (Feb 13, 2024)
13-21382968-A-C		not specified	Uncertain significance (Aug 08, 2023)
13-21382984-T-C		not specified	Uncertain significance (Jul 20, 2021)
13-21387516-T-C		not specified	Uncertain significance (Feb 17, 2024)
13-21387623-C-T		not specified	Uncertain significance (May 10, 2022)
13-21387625-C-T		not specified	Uncertain significance (Jun 13, 2023)
13-21387626-G-A		not specified	Uncertain significance (Dec 14, 2021)
13-21391815-A-G		not specified	Uncertain significance (Dec 06, 2022)
13-21391821-C-T		not specified	Uncertain significance (Aug 15, 2023)
13-21391842-C-T		not specified	Uncertain significance (Jun 23, 2021)
13-21400374-G-A		not specified	Uncertain significance (May 18, 2023)
13-21400399-A-C		not specified	Uncertain significance (Aug 12, 2022)
13-21400414-C-T		not specified	Uncertain significance (Jun 22, 2023)
13-21400465-A-G		not specified	Uncertain significance (Sep 16, 2021)
13-21413690-G-C		not specified	Uncertain significance (Apr 04, 2024)
13-21413729-A-G		not specified	Uncertain significance (Sep 12, 2023)
13-21421077-G-C		not specified	Uncertain significance (May 29, 2024)
13-21421078-C-A		not specified	Uncertain significance (May 16, 2024)
13-21421159-T-C		not specified	Likely benign (Apr 07, 2023)
13-21459072-C-T		not specified	Uncertain significance (Sep 01, 2021)
13-21459158-G-C		not specified	Uncertain significance (Sep 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC20	protein_coding	protein_coding	ENST00000382466	12	83247

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000520	0.994	124633	0	22	124655	0.0000882

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.25	125	171	0.730	0.00000901	2283
Missense in Polyphen		38	62.824	0.60486		892
Synonymous	0.692	55	61.9	0.888	0.00000329	629
Loss of Function	2.43	9	21.0	0.428	9.84e-7	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000193	0.000192
Ashkenazi Jewish	0.000105	0.0000993
East Asian	0.0000563	0.0000556
Finnish	0.0000496	0.0000464
European (Non-Finnish)	0.000121	0.000115
Middle Eastern	0.0000563	0.0000556
South Asian	0.0000343	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes palmitoylation of Cys residues on target proteins (PubMed:27153536, PubMed:29326245). Catalyzes palmitoylation of Cys residues in the cytoplasmic C-terminus of EGFR, and modulates the duration of EGFR signaling by modulating palmitoylation-dependent EGFR internalization and degradation (PubMed:27153536). Has a preference for acyl-CoA with C16 fatty acid chains (PubMed:29326245). Can also utilize acyl-CoA with C14 and C18 fatty acid chains (PubMed:29326245). {ECO:0000269|PubMed:27153536, ECO:0000269|PubMed:29326245}.

Intolerance Scores

• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.48

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.211

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc20

Gene ontology

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