ADAMTSL3

protein-coding

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

Gene summary

Predicted to be involved in extracellular matrix organization. Predicted to be active in extracellular matrix. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_207517.3

Inheritance

—

ClinVar variants

U:254B:27

Top phenotype

Squamous cell carcinoma

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr15:83,654,088-84,039,842

External References & Databases

Ensembl (ENSG00000156218)

Transcript & Mutation Effects

hg38 • Region Span ~385.8 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 ADAMTSL3 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 254

not providedTotal: 26

Squamous cell carcinomaTotal: 3

Lung adenocarcinomaTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207517.3. 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			4 clinvar	3 clinvar	4 clinvar	11
missense			248 clinvar	16 clinvar	4 clinvar	268
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	254	19	8	281

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207517.3	RefSeq	NP_997400.2	29	MANE Select
ENST00000286744.10	Ensembl	ENSP00000286744.5	29	MANE Select
NM_001301110.2	RefSeq	NP_001288039.1	29	Standard
ENST00000567476.1	Ensembl	ENSP00000456313.1	29	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

protein binding
peptidase activity

Cellular Component

extracellular region
intracellular membrane-bounded organelle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000286744
Coding exons: 29
Length: 385757
Individuals with no LoFs: 125658
Homozygous LoFs: 0
Heterozygous LoFs: 90
Defined: 125748
p: 0.000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.475	917	958	0.957	0.0000533	11061
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00015	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00044	0.00044	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00037	0.00036	rare
South Asian	0.00086	0.00082	rare
Other	0.00049	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.109

Intolerance Scores

LoFtool: 0.818
RVIS EVS: 0.33
RVIS percentile EVS: 73.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0561

Gene Damage Prediction

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