ZDHHC4

zinc finger DHHC-type palmitoyltransferase 4, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 7:6577434-6589374

Links

ENSG00000136247 ∙ NCBI:55146 ∙ ∙ HGNC:18471 ∙ Uniprot:Q9NPG8 ∙ 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 ZDHHC4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC4 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	15	2	0

Variants in ZDHHC4

This is a list of pathogenic ClinVar variants found in the ZDHHC4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-6580588-C-G		not specified	Uncertain significance (Dec 15, 2023)
7-6580628-G-A		not specified	Likely benign (Oct 20, 2021)
7-6582215-C-G		not specified	Uncertain significance (Jan 23, 2024)
7-6582240-G-C		not specified	Uncertain significance (Jun 27, 2022)
7-6583339-T-C		not specified	Uncertain significance (Mar 15, 2024)
7-6585022-G-A		not specified	Uncertain significance (Apr 06, 2024)
7-6585061-G-C		not specified	Uncertain significance (Aug 24, 2023)
7-6585068-C-G		not specified	Uncertain significance (May 10, 2023)
7-6585094-G-C		not specified	Uncertain significance (Aug 13, 2021)
7-6585141-G-A		not specified	Uncertain significance (Jun 21, 2022)
7-6585210-A-G		not specified	Likely benign (Jan 10, 2022)
7-6585256-T-C		not specified	Uncertain significance (Dec 17, 2023)
7-6588610-CT-C			Likely benign (Apr 01, 2023)
7-6588614-T-C			Likely benign (Apr 01, 2023)
7-6588625-C-G		not specified	Uncertain significance (Feb 06, 2024)
7-6588638-C-T		not specified	Uncertain significance (Mar 15, 2024)
7-6588698-T-G		not specified	Uncertain significance (Dec 27, 2022)
7-6588798-C-T		not specified	Uncertain significance (Aug 29, 2022)
7-6588822-G-A		not specified	Likely benign (Mar 18, 2024)
7-6588842-C-T		not specified	Uncertain significance (Nov 09, 2021)
7-6588846-G-A		not specified	Uncertain significance (Jan 24, 2024)
7-6588870-T-G		not specified	Uncertain significance (Mar 19, 2024)
7-6588876-C-T		not specified	Uncertain significance (Oct 24, 2023)
7-6588888-A-C		not specified	Uncertain significance (Jun 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC4	protein_coding	protein_coding	ENST00000396706	6	11941

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.30e-9	0.125	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0564	195	193	1.01	0.0000107	2241
Missense in Polyphen		62	57.716	1.0742		739
Synonymous	-0.634	88	80.8	1.09	0.00000494	685
Loss of Function	0.122	13	13.5	0.964	6.34e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.000870	0.000870
Finnish	0.00	0.00
European (Non-Finnish)	0.000167	0.000167
Middle Eastern	0.000870	0.000870
South Asian	0.000295	0.000294
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0717

Intolerance Scores

• loftool: 0.997
• rvis_EVS: 0.78
• rvis_percentile_EVS: 87.14

Haploinsufficiency Scores

• pHI: 0.0252
• hipred: N
• hipred_score: 0.144
• ghis: 0.434

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc4

Gene ontology

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