ADAMTSL1

ADAMTS like 1, the group of ADAMTS like|I-set domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 9:17906562-18910950

Previous symbols: [ "C9orf94" ]

Links

ENSG00000178031 ∙ NCBI:92949 ∙ OMIM:609198 ∙ HGNC:14632 ∙ Uniprot:Q8N6G6 ∙ 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 ADAMTSL1 gene.

• Inborn genetic diseases (96 variants)
• not provided (25 variants)
• not specified (3 variants)
• Orofacial cleft 1 (1 variants)
• ADAMTSL1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAMTSL1 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				5	7	12
missense			100	6		106
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	4	1	6
non coding						0
Total	0	0	102	11	7

Variants in ADAMTSL1

This is a list of pathogenic ClinVar variants found in the ADAMTSL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-18474252-C-G		not specified	Uncertain significance (May 11, 2022)
9-18504844-C-T		not specified	Uncertain significance (Dec 01, 2022)
9-18504856-G-A		not specified	Uncertain significance (Apr 12, 2022)
9-18504860-G-A		ADAMTSL1-related disorder	Likely benign (Mar 27, 2023)
9-18504870-A-G			Benign (Dec 31, 2019)
9-18504874-G-T		not specified	Uncertain significance (Nov 08, 2022)
9-18504875-A-C		not specified	Uncertain significance (Nov 08, 2022)
9-18504922-G-T		not specified	Uncertain significance (Aug 01, 2022)
9-18504929-A-G			Uncertain significance (Jun 15, 2022)
9-18504940-C-G		not specified	Uncertain significance (Oct 20, 2023)
9-18533259-A-G			Benign (Dec 31, 2019)
9-18533270-G-A		not specified	Uncertain significance (Dec 21, 2022)
9-18574040-C-T		not specified	Uncertain significance (Jul 06, 2022)
9-18574049-G-A		not specified	Uncertain significance (Jun 09, 2022)
9-18574073-C-T		Orofacial cleft 1	Uncertain significance (Nov 22, 2022)
9-18574095-C-A		not specified	Uncertain significance (Jan 04, 2024)
9-18574097-A-C		not specified	Uncertain significance (Aug 04, 2023)
9-18574136-C-T		not specified	Uncertain significance (Mar 22, 2023)
9-18574175-C-A			Likely benign (Oct 01, 2022)
9-18574183-G-T			Likely benign (Dec 31, 2019)
9-18622244-T-C		not specified	Uncertain significance (Nov 17, 2022)
9-18622255-G-A		not specified	Uncertain significance (Jul 14, 2023)
9-18622276-G-A		ADAMTSL1-related disorder	Likely benign (May 25, 2022)
9-18622324-C-T		not specified	Uncertain significance (Feb 23, 2023)
9-18635982-A-G		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAMTSL1	protein_coding	protein_coding	ENST00000380548	29	437057

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.12e-12	1.00	125685	0	63	125748	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.970	1138	1.05e+3	1.08	0.0000646	11297
Missense in Polyphen		406	401.45	1.0113		4321
Synonymous	-3.68	535	437	1.22	0.0000290	3562
Loss of Function	5.24	36	89.5	0.402	0.00000456	974

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000655	0.000631
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000222	0.000217
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000235	0.000229
Middle Eastern	0.000222	0.000217
South Asian	0.000431	0.000425
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.673
• rvis_EVS: -0.86
• rvis_percentile_EVS: 10.9

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.466
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adamtsl1

Gene ontology

• Biological process: proteolysis
• Cellular component: extracellular region;endoplasmic reticulum lumen
• Molecular function: peptidase activity