ADAMTS9

ADAM metallopeptidase with thrombospondin type 1 motif 9, the group of ADAM metallopeptidases with thrombospondin type 1 motif

Basic information

Region (hg38): 3:64515653-64688000

Links

ENSG00000163638 ∙ NCBI:56999 ∙ OMIM:605421 ∙ HGNC:13202 ∙ Uniprot:Q9P2N4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nephronophthisis 1 (Supportive), mode of inheritance: AR
• ciliopathy (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADAMTS9 gene.

• not provided (200 variants)
• Inborn genetic diseases (90 variants)
• ADAMTS9-related condition (4 variants)
• Nephronophthisis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTS9 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				25	17	42
missense			119	7	9	135
nonsense			2			2
start loss						0
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			1	3	3	7
non coding				9	80	89
Total	0	0	124	41	106

Variants in ADAMTS9

This is a list of pathogenic ClinVar variants found in the ADAMTS9 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-64522181-C-T		ADAMTS9-related disorder	Benign (Jan 25, 2024)
3-64522197-T-G			Uncertain significance (Sep 22, 2022)
3-64522219-T-C			Benign (Dec 07, 2023)
3-64522237-T-C		ADAMTS9-related disorder	Benign (Jan 01, 2024)
3-64522245-C-T		ADAMTS9-related disorder	Likely benign (Oct 27, 2023)
3-64522250-C-T		not specified	Uncertain significance (Apr 18, 2023)
3-64532946-G-A			Benign (May 24, 2021)
3-64533147-C-T			Likely benign (Aug 10, 2023)
3-64533167-G-A		not specified	Uncertain significance (Sep 17, 2021)
3-64533193-A-G			Likely benign (Jul 12, 2023)
3-64533203-T-C		not specified	Uncertain significance (Jun 02, 2023)
3-64533226-A-G			Likely benign (Nov 27, 2023)
3-64533238-G-C			Likely benign (Mar 08, 2023)
3-64533252-G-C		not specified	Uncertain significance (Sep 13, 2023)
3-64533267-G-T		not specified	Uncertain significance (Sep 01, 2021)
3-64533318-T-C			Benign (May 08, 2021)
3-64533480-C-T			Benign (May 08, 2021)
3-64539232-C-A			Uncertain significance (Aug 10, 2023)
3-64539236-G-A			Likely benign (Sep 07, 2022)
3-64539265-C-T		not specified	Uncertain significance (Jul 26, 2021)
3-64540891-A-G			Benign (May 10, 2021)
3-64540934-G-A			Benign (May 08, 2021)
3-64540936-T-C			Benign (May 10, 2021)
3-64540975-CCAATGTG-C			Benign (May 08, 2021)
3-64541041-G-C			Benign (May 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAMTS9	protein_coding	protein_coding	ENST00000498707	39	172344

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000100	1.00	125668	0	80	125748	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.955	1030	1.12e+3	0.920	0.0000634	12696
Missense in Polyphen		240	402.7	0.59598		4536
Synonymous	-3.09	495	415	1.19	0.0000245	3598
Loss of Function	7.13	35	119	0.294	0.00000657	1327

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000736	0.000736
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000331	0.000326
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000297	0.000281
Middle Eastern	0.000331	0.000326
South Asian	0.000505	0.000490
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves the large aggregating proteoglycans, aggrecan (at the '1838-Glu-|-Ala-1839' site) and versican (at the '1428- Glu-|-Ala-1429' site). Has a protease-independent function in promoting the transport from the endoplasmic reticulum to the Golgi apparatus of a variety of secretory cargos. {ECO:0000269|PubMed:12514189, ECO:0000269|PubMed:22419820}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Extracellular matrix organization;Degradation of the extracellular matrix;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Intolerance Scores

• loftool: 0.651
• rvis_EVS: -2.39
• rvis_percentile_EVS: 1.08

Haploinsufficiency Scores

• pHI: 0.198
• hipred: N
• hipred_score: 0.427
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.352

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adamts9
• Phenotype: embryo phenotype; pigmentation phenotype; 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); normal phenotype; reproductive system 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); vision/eye 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); limbs/digits/tail phenotype; digestive/alimentary phenotype; cellular phenotype; immune system phenotype; endocrine/exocrine gland 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; craniofacial phenotype

Zebrafish Information Network

• Gene name: adamts9
• Affected structure: pancreatic B cell
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

• Biological process: heart valve morphogenesis;ventricular cardiac muscle tissue development;proteolysis;glycoprotein catabolic process;multicellular organism development;response to bacterium;negative regulation of endothelial cell migration;protein transport;vesicle-mediated transport;extracellular matrix organization;aorta morphogenesis;positive regulation of melanocyte differentiation;endothelial cell-matrix adhesion;negative regulation of sprouting angiogenesis
• Cellular component: extracellular space;endoplasmic reticulum;cell surface;extracellular matrix;intracellular membrane-bounded organelle;collagen-containing extracellular matrix
• Molecular function: metalloendopeptidase activity;metallopeptidase activity;zinc ion binding