ADAMTS17

ADAM metallopeptidase with thrombospondin type 1 motif 17, the group of ADAM metallopeptidases with thrombospondin type 1 motif

Basic information

Region (hg38): 15:99971437-100342005

Links

ENSG00000140470 ∙ NCBI:170691 ∙ OMIM:607511 ∙ HGNC:17109 ∙ Uniprot:Q8TE56 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Weill-Marchesani 4 syndrome, recessive (Moderate), mode of inheritance: AR
• Weill-Marchesani 4 syndrome, recessive (Strong), mode of inheritance: AR
• Weill-Marchesani 4 syndrome, recessive (Supportive), mode of inheritance: AR
• Weill-Marchesani 4 syndrome, recessive (Definitive), mode of inheritance: AR
• Weill-Marchesani 4 syndrome, recessive (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Weill-Marchesan syndrome 4	AR	Ophthalmologic; Pharmacogenomic	Individuals may be at risk of glaucoma, and surveillance may allow early management and preventive measures; Agents that may contribute to glaucoma should be avoided	Musculoskeletal; Ophthalmologic	19836009; 20375329; 22486325

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADAMTS17 gene.

• not provided (22 variants)
• Weill-Marchesani 4 syndrome, recessive (2 variants)
• Anterior segment dysgenesis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTS17 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			7	231	17	255
missense		1	350	3	8	362
nonsense	10	2	1			13
start loss						0
frameshift	14	2	2			18
inframe indel			4	1		5
splice donor/acceptor (+/-2bp)		10	1			11
splice region			13	27	3	43
non coding			116	107	184	407
Total	24	15	481	342	209

Highest pathogenic variant AF is 0.0000197

Variants in ADAMTS17

This is a list of pathogenic ClinVar variants found in the ADAMTS17 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-99971468-C-A		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 12, 2018)
15-99971524-G-A		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 12, 2018)
15-99971612-G-C		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 12, 2018)
15-99971655-A-C		Weill-Marchesani 4 syndrome, recessive	Likely benign (Jan 13, 2018)
15-99971664-C-G		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 13, 2018)
15-99971680-C-T		Weill-Marchesani 4 syndrome, recessive	Benign (Jan 13, 2018)
15-99971701-C-G		Weill-Marchesani 4 syndrome, recessive	Benign (Jan 12, 2018)
15-99971712-C-T		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 12, 2018)
15-99971724-A-C		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 12, 2018)
15-99971750-T-A		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 12, 2018)
15-99971757-G-A		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 12, 2018)
15-99971765-G-C		Weill-Marchesani 4 syndrome, recessive	Likely benign (Jan 13, 2018)
15-99971773-CTGG-C		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jun 14, 2016)
15-99971786-C-T		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 12, 2018)
15-99971797-C-G		Weill-Marchesani 4 syndrome, recessive	Likely benign (Jan 13, 2018)
15-99971802-G-A		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 13, 2018)
15-99971804-A-G		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 13, 2018)
15-99971824-C-T		Weill-Marchesani 4 syndrome, recessive	Benign (Jan 12, 2018)
15-99971842-A-G		Weill-Marchesani 4 syndrome, recessive	Benign (Jan 12, 2018)
15-99971861-T-C		Weill-Marchesani 4 syndrome, recessive	Benign (Jan 13, 2018)
15-99971870-C-T		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 13, 2018)
15-99971874-A-G		Weill-Marchesani 4 syndrome, recessive	Benign (Jan 12, 2018)
15-99971891-T-C		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 12, 2018)
15-99971901-G-A		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 13, 2018)
15-99971922-C-T		Weill-Marchesani 4 syndrome, recessive	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAMTS17	protein_coding	protein_coding	ENST00000268070	22	370417

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.80e-15	1.00	125674	1	73	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.39	728	630	1.16	0.0000434	7044
Missense in Polyphen		337	307.36	1.0964		3444
Synonymous	-4.69	372	273	1.36	0.0000215	2186
Loss of Function	3.28	34	61.9	0.549	0.00000368	635

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000721	0.000691
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000382	0.000378
Middle Eastern	0.000381	0.000381
South Asian	0.000265	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Weill-Marchesani syndrome 4 (WMS4) [MIM:613195]: An autosomal recessive syndrome characterized by lenticular myopia, ectopia lentis, glaucoma, spherophakia and short stature. Brachydactyly and decreased joint flexibility are present in some patients. {ECO:0000269|PubMed:19836009, ECO:0000269|PubMed:22486325, ECO:0000269|PubMed:24940034}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.514
• rvis_EVS: -2.27
• rvis_percentile_EVS: 1.26

Haploinsufficiency Scores

• pHI: 0.247
• hipred: Y
• hipred_score: 0.544
• ghis: 0.479

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.382

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adamts17

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular region
• Molecular function: nucleic acid binding;metalloendopeptidase activity;metal ion binding