GeneBe

ZDHHC16

zinc finger DHHC-type palmitoyltransferase 16, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): 10:97446169-97457370

Links

ENSG00000171307 ∙ NCBI:84287 ∙ OMIM:616750 ∙ HGNC:20714 ∙ Uniprot:Q969W1 ∙ 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 ZDHHC16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC16 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
16
clinvar
 16
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
 1
splice region
0
non coding
0
Total 0 0 17 0 0

Variants in ZDHHC16

This is a list of pathogenic ClinVar variants found in the ZDHHC16 region.

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

Position Type Phenotype Significance ClinVar
10-97451713-G-A not specified Uncertain significance (Apr 07, 2023)2535184
10-97451724-C-G not specified Uncertain significance (Oct 13, 2021)2255358
10-97451724-C-T not specified Uncertain significance (Jun 07, 2024)2228666
10-97451775-G-A not specified Uncertain significance (Nov 14, 2023)3192673
10-97451776-G-A not specified Uncertain significance (Mar 02, 2023)2466766
10-97451853-G-A not specified Uncertain significance (Mar 19, 2024)3334235
10-97451905-G-A not specified Uncertain significance (May 18, 2023)2548950
10-97451909-G-C not specified Uncertain significance (Feb 16, 2023)2485630
10-97452133-C-T not specified Uncertain significance (Jun 11, 2021)2232328
10-97452136-T-C not specified Uncertain significance (Feb 06, 2024)3192674
10-97452414-G-C Uncertain significance (Mar 01, 2017)806555
10-97452430-G-A not specified Uncertain significance (Mar 02, 2023)2493190
10-97452450-G-C not specified Uncertain significance (Mar 05, 2024)3192675
10-97453814-G-A not specified Uncertain significance (Jan 06, 2023)2460350
10-97454748-T-G not specified Uncertain significance (Aug 12, 2021)2244351
10-97454751-G-A not specified Uncertain significance (Mar 17, 2023)2509219
10-97455998-G-A not specified Uncertain significance (Jul 09, 2021)2235741
10-97456833-T-C not specified Uncertain significance (Jun 24, 2022)2296236

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ZDHHC16protein_codingprotein_codingENST00000393760 1011201
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.0001650.9991257190291257480.000115
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7742002330.8570.00001422444
Missense in Polyphen6483.6770.76484937
Synonymous-0.1618987.11.020.00000491764
Loss of Function2.821126.80.4110.00000173237

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003370.000337
Ashkenazi Jewish0.0001980.000198
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.0001240.000123
Middle Eastern0.000.00
South Asian0.0001630.000163
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Palmitoyl acyltransferase that mediates palmitoylation of proteins such as PLN and ZDHHC6 (PubMed:28826475). Required during embryonic heart development and cardiac function, possibly by mediating palmitoylation of PLN, thereby affecting PLN phosphorylation and homooligomerization (By similarity). Also required for eye development (By similarity). Palmitoylates ZDHHC6, affecting the quaternary assembly of ZDHHC6, its localization, stability and function (PubMed:28826475). May play a role in DNA damage response (By similarity). May be involved in apoptosis regulation (By similarity). Involved in the proliferation of neural stem cells by regulating the FGF/ERK pathway (By similarity). {ECO:0000250|UniProtKB:B8A4F0, ECO:0000250|UniProtKB:Q9ESG8, ECO:0000269|PubMed:28826475}.;

Recessive Scores

pRec
0.111

Intolerance Scores

loftool
0.470
rvis_EVS
-0.91
rvis_percentile_EVS
9.9

Haploinsufficiency Scores

pHI
0.164
hipred
N
hipred_score
0.343
ghis
0.628

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.963

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Zdhhc16
Phenotype
growth/size/body region phenotype; muscle phenotype; vision/eye 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); 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); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
zdhhc16a
Affected structure
anterior neural plate
Phenotype tag
abnormal
Phenotype quality
aplastic/hypoplastic

Gene ontology

Biological process
eye development;apoptotic process;cellular response to DNA damage stimulus;heart development;protein palmitoylation;telencephalon development
Cellular component
endoplasmic reticulum membrane;Golgi apparatus;integral component of membrane
Molecular function
protein binding;palmitoyltransferase activity;protein-cysteine S-palmitoyltransferase activity