ZDHHC2

zinc finger DHHC-type palmitoyltransferase 2, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 8:17156481-17224799

Links

ENSG00000104219 ∙ NCBI:51201 ∙ OMIM:618621 ∙ HGNC:18469 ∙ Uniprot:Q9UIJ5 ∙ 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 ZDHHC2 gene.

• Inborn genetic diseases (23 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC2 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
missense			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	3	0

Variants in ZDHHC2

This is a list of pathogenic ClinVar variants found in the ZDHHC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-17156739-C-T		not specified	Uncertain significance (Nov 09, 2023)
8-17156752-C-T		not specified	Likely benign (Apr 07, 2023)
8-17156784-A-G		not specified	Uncertain significance (Mar 07, 2023)
8-17156790-G-C		not specified	Uncertain significance (Nov 17, 2022)
8-17156790-G-T		not specified	Uncertain significance (Feb 23, 2023)
8-17156803-C-G		not specified	Likely benign (Apr 07, 2023)
8-17156808-C-T			Likely benign (Oct 01, 2022)
8-17156815-G-C		not specified	Uncertain significance (Jan 04, 2024)
8-17156815-G-T		not specified	Uncertain significance (Dec 06, 2021)
8-17184809-G-A		not specified	Uncertain significance (Aug 26, 2022)
8-17184809-G-C		not specified	Uncertain significance (Apr 07, 2022)
8-17186331-T-C		not specified	Uncertain significance (Oct 13, 2023)
8-17186333-G-A		not specified	Uncertain significance (May 27, 2022)
8-17186349-A-G		not specified	Uncertain significance (Jan 10, 2023)
8-17195565-A-G		not specified	Uncertain significance (Apr 18, 2023)
8-17197588-G-A		not specified	Uncertain significance (Jun 01, 2023)
8-17197600-G-T		not specified	Uncertain significance (Jun 30, 2023)
8-17205663-A-G		not specified	Uncertain significance (Mar 02, 2023)
8-17205759-T-G		not specified	Uncertain significance (Dec 15, 2022)
8-17207973-A-G		not specified	Uncertain significance (Oct 13, 2021)
8-17207987-T-G		not specified	Uncertain significance (Apr 20, 2023)
8-17208020-A-T		not specified	Uncertain significance (Jan 29, 2024)
8-17208083-T-C		not specified	Uncertain significance (Apr 27, 2023)
8-17209944-G-C		not specified	Uncertain significance (Feb 10, 2022)
8-17210447-C-G		not specified	Uncertain significance (Jan 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC2	protein_coding	protein_coding	ENST00000262096	12	68771

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00100	0.997	124581	0	54	124635	0.000217

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.296	178	167	1.06	0.00000790	2393
Missense in Polyphen		66	66.142	0.99785		1003
Synonymous	-2.17	79	58.0	1.36	0.00000288	642
Loss of Function	2.67	9	22.8	0.395	0.00000127	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000447	0.000447
Ashkenazi Jewish	0.000101	0.0000994
East Asian	0.0000558	0.0000556
Finnish	0.00116	0.00111
European (Non-Finnish)	0.000100	0.0000973
Middle Eastern	0.0000558	0.0000556
South Asian	0.0000669	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Palmitoyltransferase specific for GAP43 and DLG4/PSD95. {ECO:0000250}.
• Pathway: Surfactant metabolism;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.0886

Intolerance Scores

• loftool: 0.695
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.01

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.289
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc2
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

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