ZDHHC13

zinc finger DHHC-type palmitoyltransferase 13, the group of Zinc fingers DHHC-type|Ankyrin repeat domain containing

Basic information

Region (hg38): 11:19117099-19176422

Links

ENSG00000177054 ∙ NCBI:54503 ∙ OMIM:612815 ∙ HGNC:18413 ∙ Uniprot:Q8IUH4 ∙ 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 ZDHHC13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC13 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in ZDHHC13

This is a list of pathogenic ClinVar variants found in the ZDHHC13 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-19117257-G-C		not specified	Uncertain significance (Dec 19, 2023)
11-19143012-G-C		not specified	Uncertain significance (Feb 23, 2023)
11-19143017-G-A		not specified	Uncertain significance (Dec 28, 2023)
11-19143021-G-A		not specified	Uncertain significance (Apr 07, 2022)
11-19143027-G-A		not specified	Uncertain significance (Apr 23, 2024)
11-19147651-A-T		not specified	Uncertain significance (Jun 16, 2023)
11-19149187-A-G		not specified	Likely benign (Jun 13, 2024)
11-19149225-A-G		not specified	Uncertain significance (May 16, 2023)
11-19149302-A-G		not specified	Uncertain significance (Oct 04, 2022)
11-19149307-A-G		not specified	Uncertain significance (Oct 25, 2022)
11-19149315-T-G		not specified	Uncertain significance (Dec 21, 2023)
11-19150748-A-G		not specified	Uncertain significance (May 11, 2022)
11-19150758-C-T		not specified	Uncertain significance (Feb 12, 2024)
11-19150781-A-G		not specified	Uncertain significance (Sep 14, 2022)
11-19152592-A-C		not specified	Uncertain significance (Dec 19, 2022)
11-19152600-G-C		not specified	Uncertain significance (Sep 29, 2023)
11-19152615-G-A		not specified	Uncertain significance (Apr 11, 2023)
11-19152682-G-A		not specified	Uncertain significance (Apr 01, 2024)
11-19155815-T-C		not specified	Uncertain significance (Jun 22, 2022)
11-19155839-T-C		not specified	Uncertain significance (Dec 17, 2021)
11-19155856-T-C		not specified	Uncertain significance (Apr 19, 2024)
11-19155893-T-C		not specified	Uncertain significance (Jan 03, 2024)
11-19163329-A-G		not specified	Uncertain significance (Jun 21, 2022)
11-19163404-G-A			Likely benign (Feb 14, 2018)
11-19165098-G-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC13	protein_coding	protein_coding	ENST00000446113	17	59324

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-19	0.00935	124530	0	108	124638	0.000433

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.752	256	292	0.876	0.0000133	4057
Missense in Polyphen		74	81.52	0.90776		1155
Synonymous	-0.228	103	100	1.03	0.00000449	1132
Loss of Function	0.512	31	34.2	0.906	0.00000175	438

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.000944
Ashkenazi Jewish	0.000698	0.000696
East Asian	0.000418	0.000389
Finnish	0.0000465	0.0000464
European (Non-Finnish)	0.000528	0.000513
Middle Eastern	0.000418	0.000389
South Asian	0.000437	0.000425
Other	0.000176	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Palmitoyltransferase for HTT and GAD2. May play a role in Mg(2+) transport. {ECO:0000250|UniProtKB:Q9CWU2}.

Recessive Scores

• pRec: 0.0740

Intolerance Scores

• loftool: 0.938
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.55

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.251
• ghis: 0.393

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000672

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc13
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; skeleton phenotype; renal/urinary system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype

Zebrafish Information Network

• Gene name: zdhhc13
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: positive regulation of I-kappaB kinase/NF-kappaB signaling;magnesium ion transmembrane transport
• Cellular component: Golgi membrane;endoplasmic reticulum;membrane;integral component of membrane;cytoplasmic vesicle membrane;Golgi-associated vesicle membrane
• Molecular function: magnesium ion transmembrane transporter activity;palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity