ADAMTS19

ADAM metallopeptidase with thrombospondin type 1 motif 19, the group of ADAM metallopeptidases with thrombospondin type 1 motif

Basic information

Region (hg38): 5:129460280-129738683

Links

ENSG00000145808 ∙ NCBI:171019 ∙ OMIM:607513 ∙ HGNC:17111 ∙ Uniprot:Q8TE59 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cardiac valvular dysplasia 2 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cardiac valvular dysplasia 2	AR	Cardiovascular	The condition can involve multiple types of cardiovascular anomalies, and awareness may allow early management	Cardiovascular	31844321; 32323311

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADAMTS19 gene.

• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTS19 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				4	1	5
missense			62	3	2	67
nonsense	1	1	1			3
start loss						0
frameshift	2					2
inframe indel					1	1
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding			1	1		2
Total	3	1	65	8	4

Variants in ADAMTS19

This is a list of pathogenic ClinVar variants found in the ADAMTS19 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-129461108-A-T		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
5-129461122-C-G		ADAMTS19-related disorder • Inborn genetic diseases	Conflicting classifications of pathogenicity (Mar 28, 2023)
5-129461123-G-T		Inborn genetic diseases	Uncertain significance (Nov 21, 2022)
5-129461137-G-A		Inborn genetic diseases	Uncertain significance (Dec 06, 2021)
5-129461150-C-G		Inborn genetic diseases	Uncertain significance (Sep 09, 2021)
5-129461150-C-T		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
5-129461167-C-A		Inborn genetic diseases	Uncertain significance (Jun 22, 2021)
5-129461227-G-C		Inborn genetic diseases	Uncertain significance (Jan 10, 2023)
5-129461245-CGG-C			Pathogenic (Jun 27, 2022)
5-129461261-G-A		Inborn genetic diseases	Uncertain significance (May 29, 2024)
5-129461279-GC-G			Pathogenic (Jun 27, 2022)
5-129461311-G-A		Inborn genetic diseases	Uncertain significance (May 04, 2022)
5-129461321-G-C		Inborn genetic diseases	Uncertain significance (Dec 13, 2022)
5-129461345-C-T		Inborn genetic diseases	Uncertain significance (May 31, 2023)
5-129461392-C-G		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
5-129461417-C-A		not specified	Uncertain significance (Mar 29, 2024)
5-129461426-C-G		Inborn genetic diseases	Uncertain significance (Dec 08, 2023)
5-129461449-C-A		Inborn genetic diseases	Uncertain significance (Mar 31, 2022)
5-129461462-C-T		Inborn genetic diseases	Uncertain significance (Jan 29, 2024)
5-129461471-C-A		Inborn genetic diseases	Uncertain significance (Apr 23, 2024)
5-129461485-C-T		Inborn genetic diseases	Uncertain significance (Apr 23, 2024)
5-129461507-C-T		Inborn genetic diseases	Uncertain significance (Jun 10, 2024)
5-129461521-G-C		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
5-129461565-G-C			Benign (Jul 05, 2018)
5-129461578-G-A		ADAMTS19-related disorder	Likely benign (Jul 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAMTS19	protein_coding	protein_coding	ENST00000274487	23	278419

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.96e-8	1.00	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.10	451	595	0.758	0.0000291	7814
Missense in Polyphen		122	230.94	0.52828		2815
Synonymous	-0.0872	206	204	1.01	0.00000999	2277
Loss of Function	4.54	24	62.9	0.382	0.00000344	768

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000550	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000259	0.000255
Middle Eastern	0.0000550	0.0000544
South Asian	0.000238	0.000229
Other	0.000347	0.000326

dbNSFP

Source: dbNSFP

• Pathway: Post-translational protein modification;Metabolism of proteins;O-glycosylation of TSR domain-containing proteins;O-linked glycosylation (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.440
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.93

Haploinsufficiency Scores

• pHI: 0.336
• hipred: Y
• hipred_score: 0.685
• ghis: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.256

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adamts19
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

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