ZDHHC9

zinc finger DHHC-type palmitoyltransferase 9, the group of Zinc fingers DHHC-type

Basic information

Region (hg38): X:129803287-129843909

Previous symbols: [ "ZDHHC10", "CXorf11" ]

Links

ENSG00000188706 ∙ NCBI:51114 ∙ OMIM:300646 ∙ HGNC:18475 ∙ Uniprot:Q9Y397 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• syndromic X-linked intellectual disability Raymond type (Definitive), mode of inheritance: XLR
• syndromic X-linked intellectual disability Raymond type (Strong), mode of inheritance: XL
• X-linked intellectual disability with marfanoid habitus (Supportive), mode of inheritance: XL
• syndromic X-linked intellectual disability Raymond type (Definitive), mode of inheritance: XL
• syndromic X-linked intellectual disability Raymond type (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked syndromic, Raymond type	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Musculoskeletal; Neurologic	17436253; 19377476

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZDHHC9 gene.

• Syndromic X-linked intellectual disability Raymond type (160 variants)
• not provided (43 variants)
• Inborn genetic diseases (14 variants)
• not specified (8 variants)
• Intellectual disability (3 variants)
• ZDHHC9-related condition (2 variants)
• Neurodevelopmental disorder (1 variants)
• History of neurodevelopmental disorder (1 variants)
• See cases (1 variants)
• Autism spectrum disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZDHHC9 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			2	39	4	45
missense		4	68	7	2	81
nonsense	1	2	1			4
start loss						0
frameshift	3	2	1			6
inframe indel				1		1
splice donor/acceptor (+/-2bp)	1	1	1			3
splice region			2	9	1	12
non coding				18	29	47
Total	5	9	73	65	35

Variants in ZDHHC9

This is a list of pathogenic ClinVar variants found in the ZDHHC9 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-129806265-G-A			Benign (May 20, 2021)
X-129806366-T-C		Inborn genetic diseases	Likely benign (Oct 10, 2016)
X-129806381-C-G		Syndromic X-linked intellectual disability Raymond type	Uncertain significance (Jul 27, 2023)
X-129806384-C-T		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
X-129806390-C-T		Syndromic X-linked intellectual disability Raymond type	Uncertain significance (Jul 19, 2022)
X-129806400-T-TGGCTGTGGG		Syndromic X-linked intellectual disability Raymond type	Likely benign (Jan 30, 2024)
X-129806409-G-A		Syndromic X-linked intellectual disability Raymond type	Likely benign (Jan 30, 2024)
X-129806410-G-C		Syndromic X-linked intellectual disability Raymond type	Uncertain significance (Jan 19, 2021)
X-129806411-G-T		Syndromic X-linked intellectual disability Raymond type	Uncertain significance (Aug 31, 2021)
X-129806420-G-A		Syndromic X-linked intellectual disability Raymond type	Conflicting classifications of pathogenicity (Oct 07, 2022)
X-129806427-C-T		Syndromic X-linked intellectual disability Raymond type	Likely benign (Aug 19, 2022)
X-129806431-T-G		Inborn genetic diseases • Syndromic X-linked intellectual disability Raymond type	Conflicting classifications of pathogenicity (Jul 13, 2023)
X-129806432-C-T		Syndromic X-linked intellectual disability Raymond type	Benign (Nov 15, 2023)
X-129806433-G-A		Syndromic X-linked intellectual disability Raymond type	Benign (Sep 26, 2023)
X-129806433-G-C		Syndromic X-linked intellectual disability Raymond type	Likely benign (Feb 22, 2022)
X-129806435-G-A		Syndromic X-linked intellectual disability Raymond type	Likely benign (Oct 14, 2022)
X-129806437-G-A		Syndromic X-linked intellectual disability Raymond type	Uncertain significance (Nov 23, 2020)
X-129806440-C-T		Syndromic X-linked intellectual disability Raymond type	Uncertain significance (Jul 05, 2022)
X-129806444-T-C		Syndromic X-linked intellectual disability Raymond type	Uncertain significance (May 21, 2022)
X-129806451-C-T		Syndromic X-linked intellectual disability Raymond type	Benign (Jan 12, 2024)
X-129806452-G-A		Syndromic X-linked intellectual disability Raymond type	Uncertain significance (Sep 30, 2023)
X-129806462-T-A		Syndromic X-linked intellectual disability Raymond type	Uncertain significance (Aug 11, 2023)
X-129806464-G-A		Syndromic X-linked intellectual disability Raymond type	Uncertain significance (Oct 31, 2018)
X-129806476-T-C		Syndromic X-linked intellectual disability Raymond type	Uncertain significance (Aug 14, 2020)
X-129806478-T-G		Syndromic X-linked intellectual disability Raymond type	Benign (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZDHHC9	protein_coding	protein_coding	ENST00000357166	9	40622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.737	0.262	125742	1	3	125746	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.55	66	156	0.424	0.0000127	2396
Missense in Polyphen		20	72.664	0.27524		1041
Synonymous	-1.17	68	56.8	1.20	0.00000459	718
Loss of Function	2.85	2	13.1	0.152	0.00000111	201

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000760	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000625	0.0000462
European (Non-Finnish)	0.0000245	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The ZDHHC9-GOLGA7 complex is a palmitoyltransferase specific for HRAS and NRAS. {ECO:0000269|PubMed:16000296}.
• Disease: DISEASE: Mental retardation, X-linked, syndromic, ZDHHC9-related (MRXSZ) [MIM:300799]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Some MRXSZ patients have marfanoid habitus as an additional feature. {ECO:0000269|PubMed:17436253, ECO:0000269|PubMed:19377476}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0958

Intolerance Scores

• loftool: 0.377
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.610
• hipred: Y
• hipred_score: 0.662
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zdhhc9

Gene ontology

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