STAMBPL1

protein-coding

STAM binding protein like 1, the group of JAMM/MPN+ metallopeptidase family

Gene summary

Enables K63-linked deubiquitinase activity. Involved in cellular response to L-leucine and positive regulation of TORC1 signaling. Located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020799.4

Inheritance

—

ClinVar variants

U:59B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr10:88,879,734-88,975,153

External References & Databases

Ensembl (ENSG00000138134)

Transcript & Mutation Effects

hg38 • Region Span ~95.4 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 STAMBPL1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 60

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020799.4. 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				1 clinvar		1
missense			58 clinvar	3 clinvar		61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	59	4	0	63

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020799.4	RefSeq	NP_065850.1	10	MANE Select
ENST00000371926.8	Ensembl	ENSP00000360994.3	10	MANE Select
ENST00000371924.5	Ensembl	ENSP00000360992.1	10	Standard
ENST00000371927.7	Ensembl	ENSP00000360995.3	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

TGF-beta Signaling Pathway
TGF_beta_Receptor

Biological Process

protein deubiquitination
protein K63-linked deubiquitination

Molecular Function

thiol-dependent ubiquitin-specific protease activity
protein binding
metallopeptidase activity
metal ion binding
Lys63-specific deubiquitinase activity

Cellular Component

endosome
cytosol
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371926
Coding exons: 10
Length: 95420
Individuals with no LoFs: 125695
Homozygous LoFs: 0
Heterozygous LoFs: 44
Defined: 125739
p: 0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.266	221	232	0.951	0.0000117	2877
Missense (PolyPhen)		69	87.113	0.79208		1002
Synonymous	0.388	77	81.5	0.945	0.00000412	791
Loss of Function	0.488	23	25.7	0.896	0.00000168	282

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00026	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00038	0.00038	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.000099	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Zinc metalloprotease that specifically cleaves 'Lys-63'- linked polyubiquitin chains. Does not cleave 'Lys-48'-linked polyubiquitin chains. {ECO:0000269|PubMed:18758443}.;

Recessive Scores

pRec: 0.0986

Intolerance Scores

LoFtool: 0.731
RVIS EVS: 0.04
RVIS percentile EVS: 57.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.688

Gene Damage Prediction

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