ADAMTS9

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

Basic information

Region (hg38): 3:64515654-64688000

Links

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

Phenotypes

GenCC

Source: genCC

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

ClinVar

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

• not_specified (293 variants)
• not_provided (203 variants)
• ADAMTS9-related_disorder (38 variants)
• Nephronophthisis (2 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. These statistics are base on transcript: NM_000182920.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			4	47	16	67
missense			318	17	10	345
nonsense			3			3
start loss						0
frameshift		1	1			2
splice donor/acceptor (+/-2bp)			3			3
Total	0	1	329	64	26

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
		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

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

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