ADAMTSL3

ADAMTS like 3, the group of I-set domain containing|Immunoglobulin like domain containing|ADAMTS like

Basic information

Region (hg38): 15:83654087-84039842

Links

ENSG00000156218 ∙ NCBI:57188 ∙ OMIM:609199 ∙ HGNC:14633 ∙ Uniprot:P82987 ∙ 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 ADAMTSL3 gene.

• not provided (94 variants)
• Inborn genetic diseases (68 variants)
• Squamous cell carcinoma (3 variants)
• Lung adenocarcinoma (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTSL3 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				3	8	11
missense			65	5	12	82
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			4		69	73
Total	0	0	69	8	89

Variants in ADAMTSL3

This is a list of pathogenic ClinVar variants found in the ADAMTSL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-83655689-G-A			Benign (Nov 10, 2018)
15-83655774-A-T		not specified	Uncertain significance (Jan 26, 2022)
15-83655775-C-T		not specified	Uncertain significance (Dec 21, 2022)
15-83655788-G-T		not specified	Uncertain significance (Dec 18, 2023)
15-83655819-C-T		not specified	Uncertain significance (Mar 22, 2023)
15-83655829-A-T		not specified	Uncertain significance (Dec 19, 2022)
15-83704176-G-A			Benign (Jun 18, 2021)
15-83704405-C-A			Likely benign (May 16, 2018)
15-83704567-C-CAG			Benign (Nov 10, 2018)
15-83704618-G-A			Benign (Nov 10, 2018)
15-83773520-T-C			Benign (Nov 10, 2018)
15-83773545-A-G		not specified	Uncertain significance (Mar 22, 2022)
15-83804407-T-C		Lung adenocarcinoma	Uncertain significance (Jun 06, 2022)
15-83804411-T-C			Benign (Nov 10, 2018)
15-83804753-A-G			Benign (Jun 18, 2021)
15-83804779-G-A			Benign (Nov 10, 2018)
15-83819661-CA-C			Benign (Jun 18, 2021)
15-83819777-T-C			Benign (Nov 10, 2018)
15-83819825-T-A		not specified	Uncertain significance (Nov 07, 2022)
15-83819827-C-T		not specified	Uncertain significance (Feb 10, 2022)
15-83819884-A-G			Benign (Nov 10, 2018)
15-83819905-G-A		not specified	Uncertain significance (Jan 02, 2024)
15-83820010-C-T		not specified	Uncertain significance (Mar 01, 2023)
15-83820297-C-G			Benign (Nov 10, 2018)
15-83837802-G-GA			Benign (Jun 18, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAMTSL3	protein_coding	protein_coding	ENST00000286744	29	385757

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.37e-19	1.00	125658	0	90	125748	0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.475	917	958	0.957	0.0000533	11061
Missense in Polyphen		327	363.4	0.89983		4128
Synonymous	0.294	339	346	0.980	0.0000193	3230
Loss of Function	4.39	47	92.6	0.507	0.00000494	1045

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000392	0.000392
Ashkenazi Jewish	0.00	0.00
East Asian	0.000437	0.000435
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000366	0.000360
Middle Eastern	0.000437	0.000435
South Asian	0.000857	0.000817
Other	0.000489	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: 0.109

Intolerance Scores

• loftool: 0.818
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.63

Haploinsufficiency Scores

• pHI: 0.298
• hipred: N
• hipred_score: 0.475
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0561

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adamtsl3

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular region;intracellular membrane-bounded organelle
• Molecular function: protein binding;peptidase activity