ADAMTSL1

protein-coding

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

Gene summary

This gene encodes a secreted protein and member of the ADAMTS (a disintegrin and metalloproteinase with thrombospondin motif) family. This protein lacks the metalloproteinase and disintegrin-like domains, which are typical of the ADAMTS family, but contains other ADAMTS domains, including the thrombospondin type 1 motif. This protein may have important functions in the extracellular matrix. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2008]

Previous symbols:

C9orf94

MANE transcript

NM_001040272.6

Inheritance

—

ClinVar variants

U:338B:35

Top phenotype

ADAMTSL1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr9:17,906,563-18,910,950

External References & Databases

Ensembl (ENSG00000178031)

Transcript & Mutation Effects

hg38 • Region Span ~1,004.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ADAMTSL1 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 331

not providedTotal: 31

ADAMTSL1-related disorderTotal: 11

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Orofacial cleft 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001040272.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	10 clinvar	7 clinvar	22
missense			329 clinvar	18 clinvar		347
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	338	28	7	373

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001040272.6	RefSeq	NP_001035362.3	29	MANE Select
ENST00000380548.9	Ensembl	ENSP00000369921.4	29	MANE Select
NM_052866.5	RefSeq	NP_443098.3	13	Standard
ENST00000276935.6	Ensembl	ENSP00000276935.5	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational protein modification
Metabolism of proteins
O-glycosylation of TSR domain-containing proteins
O-linked glycosylation

Biological Process

proteolysis

Molecular Function

peptidase activity

Cellular Component

extracellular region
endoplasmic reticulum lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380548
Coding exons: 29
Length: 437057
Individuals with no LoFs: 125685
Homozygous LoFs: 0
Heterozygous LoFs: 63
Defined: 125748
p: 0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.970	1138	1.05e+3	1.08	0.0000646	11297
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00039	0.00037	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00022	0.00022	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00024	0.00023	rare
South Asian	0.00043	0.00042	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.673
RVIS EVS: -0.86
RVIS percentile EVS: 10.9

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.162

Gene Damage Prediction

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