ZDHHC7

zinc finger DHHC-type palmitoyltransferase 7, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 16:84974174-85011535

Links

ENSG00000153786 ∙ NCBI:55625 ∙ OMIM:614604 ∙ HGNC:18459 ∙ Uniprot:Q9NXF8 ∙ 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 ZDHHC7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC7 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in ZDHHC7

This is a list of pathogenic ClinVar variants found in the ZDHHC7 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-84976359-G-C		not specified	Uncertain significance (Dec 22, 2023)
16-84976368-T-C		not specified	Uncertain significance (May 08, 2024)
16-84976401-A-T		not specified	Uncertain significance (Dec 21, 2023)
16-84976407-A-G		not specified	Uncertain significance (Jan 10, 2022)
16-84976434-G-A		not specified	Uncertain significance (Jul 25, 2023)
16-84976438-G-A		not specified	Uncertain significance (May 03, 2023)
16-84976479-C-T		not specified	Uncertain significance (Dec 20, 2023)
16-84976481-C-A		not specified	Uncertain significance (Apr 27, 2022)
16-84977932-T-A		not specified	Uncertain significance (Feb 16, 2023)
16-84979278-T-C		not specified	Uncertain significance (May 17, 2023)
16-84981883-C-A		not specified	Uncertain significance (Apr 18, 2023)
16-84981969-G-A		not specified	Uncertain significance (Mar 07, 2024)
16-84981978-C-T		not specified	Uncertain significance (Nov 09, 2023)
16-84990364-G-C		not specified	Uncertain significance (Jan 08, 2024)
16-84990372-C-T		not specified	Uncertain significance (Mar 04, 2024)
16-84990383-G-C		not specified	Uncertain significance (Dec 22, 2023)
16-84990419-A-T		not specified	Uncertain significance (Oct 25, 2022)
16-84990486-C-T		not specified	Uncertain significance (May 05, 2023)
16-84990492-G-A		not specified	Uncertain significance (Dec 19, 2023)
16-84990506-C-T		not specified	Uncertain significance (May 02, 2024)
16-84990507-G-A		not specified	Uncertain significance (Oct 29, 2021)
16-84990516-C-T		not specified	Uncertain significance (Oct 22, 2021)
16-84990562-T-A		not specified	Uncertain significance (Dec 18, 2023)
16-84990575-G-C		not specified	Uncertain significance (Sep 21, 2023)
16-84990601-G-C		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC7	protein_coding	protein_coding	ENST00000564466	7	37355

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000978	0.988	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.598	191	216	0.885	0.0000131	2248
Missense in Polyphen		72	103.03	0.69884		1062
Synonymous	-1.32	105	89.1	1.18	0.00000616	686
Loss of Function	2.24	8	18.3	0.437	0.00000112	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Palmitoyltransferase with broad specificity (PubMed:22031296, PubMed:28196865). Palmitoylates JAM3 (PubMed:28196865). Palmitoylates SNAP25 and DLG4/PSD95 (By similarity). Palmitoylates sex steroid hormone receptors, including ESR1, PGR and AR, thereby regulating their targeting to the plasma membrane and their function in rapid intracellular signaling upon binding of sex hormones (PubMed:22031296). May play a role in follicle stimulation hormone (FSH) activation of testicular Sertoli cells (By similarity). {ECO:0000250|UniProtKB:Q91WU6, ECO:0000250|UniProtKB:Q923G5, ECO:0000269|PubMed:22031296, ECO:0000269|PubMed:28196865}.

Recessive Scores

• pRec: 0.0945

Intolerance Scores

• loftool: 0.590
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.0903
• hipred: N
• hipred_score: 0.289
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.347

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc7

Gene ontology

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