ADAMTS16

ADAM metallopeptidase with thrombospondin type 1 motif 16, the group of ADAM metallopeptidases with thrombospondin type 1 motif

Basic information

Region (hg38): 5:5140329-5320304

Links

ENSG00000145536 ∙ NCBI:170690 ∙ OMIM:607510 ∙ HGNC:17108 ∙ Uniprot:Q8TE57 ∙ 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 ADAMTS16 gene.

• Inborn genetic diseases (55 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTS16 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				6		6
missense			54	1	1	56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	54	7	1

Variants in ADAMTS16

This is a list of pathogenic ClinVar variants found in the ADAMTS16 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-5140481-C-T		not specified	Uncertain significance (Dec 27, 2023)
5-5140672-G-T			Likely benign (Jan 01, 2023)
5-5140692-C-T		not specified	Uncertain significance (Nov 09, 2023)
5-5140697-G-T		not specified	Likely benign (Jan 23, 2023)
5-5140734-C-T		not specified	Uncertain significance (Nov 08, 2022)
5-5140746-C-G		not specified	Uncertain significance (Sep 17, 2021)
5-5146192-A-G		not specified	Uncertain significance (Jun 12, 2023)
5-5146208-G-A		not specified	Uncertain significance (Oct 29, 2021)
5-5146238-A-G		not specified	Uncertain significance (Oct 26, 2021)
5-5146285-G-T		not specified	Uncertain significance (Feb 05, 2024)
5-5146414-C-T		not specified	Uncertain significance (Oct 27, 2022)
5-5182062-G-A		not specified	Uncertain significance (May 18, 2022)
5-5182083-A-G		not specified	Uncertain significance (Oct 05, 2023)
5-5182085-G-T		not specified	Uncertain significance (Jun 02, 2023)
5-5182092-C-T		not specified	Uncertain significance (Jan 18, 2023)
5-5182129-A-G		not specified	Uncertain significance (Sep 16, 2021)
5-5182149-G-A		not specified	Likely benign (Feb 21, 2024)
5-5182182-C-G		not specified	Uncertain significance (Aug 12, 2021)
5-5182251-G-A		not specified	Uncertain significance (Jun 18, 2021)
5-5182257-C-T		not specified	Uncertain significance (Jul 08, 2022)
5-5186100-A-G		not specified	Uncertain significance (Dec 07, 2021)
5-5186123-C-T		not specified	Uncertain significance (Aug 02, 2021)
5-5186124-G-T		not specified	Uncertain significance (Mar 02, 2023)
5-5186211-A-G		not specified	Uncertain significance (Aug 10, 2021)
5-5187717-T-A			Likely benign (Mar 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAMTS16	protein_coding	protein_coding	ENST00000274181	23	179975

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000446	1.00	124801	0	50	124851	0.000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.408	682	713	0.957	0.0000420	7919
Missense in Polyphen		221	266.09	0.83055		2992
Synonymous	-1.32	305	277	1.10	0.0000174	2362
Loss of Function	5.26	19	64.7	0.294	0.00000333	754

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000274	0.000274
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.000225	0.000222
Finnish	0.000383	0.000371
European (Non-Finnish)	0.000213	0.000212
Middle Eastern	0.000225	0.000222
South Asian	0.000171	0.000163
Other	0.000182	0.000165

dbNSFP

Source: dbNSFP

• 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)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.463
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.77

Haploinsufficiency Scores

• pHI: 0.156
• hipred: Y
• hipred_score: 0.527
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.187

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adamts16

Zebrafish Information Network

• Gene name: adamts16
• Affected structure: optic cup
• Phenotype tag: abnormal
• Phenotype quality: decreased rate

Gene ontology

• Biological process: branching involved in ureteric bud morphogenesis;regulation of systemic arterial blood pressure;proteolysis;male gamete generation;regulation of cilium assembly
• Cellular component: extracellular region
• Molecular function: metalloendopeptidase activity;metal ion binding