STAMBPL1

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

Basic information

Region (hg38): 10:88879734-88975153

Links

ENSG00000138134 ∙ NCBI:57559 ∙ OMIM:612352 ∙ HGNC:24105 ∙ Uniprot:Q96FJ0 ∙ 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 STAMBPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STAMBPL1 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						0
missense			19	2		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in STAMBPL1

This is a list of pathogenic ClinVar variants found in the STAMBPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-88901717-G-T		not specified	Uncertain significance (May 10, 2022)
10-88905480-C-T		not specified	Uncertain significance (Oct 06, 2021)
10-88908731-G-A		not specified	Uncertain significance (Jul 20, 2021)
10-88910920-T-C		not specified	Uncertain significance (Apr 09, 2024)
10-88910923-A-C		not specified	Uncertain significance (Nov 19, 2022)
10-88910935-T-C		not specified	Uncertain significance (May 24, 2024)
10-88910942-G-C		not specified	Uncertain significance (Jan 30, 2024)
10-88910982-G-A		not specified	Likely benign (Sep 26, 2023)
10-88910988-T-C		not specified	Uncertain significance (Apr 06, 2024)
10-88913108-A-G		not specified	Uncertain significance (Oct 12, 2021)
10-88913182-C-T		not specified	Uncertain significance (Oct 12, 2022)
10-88913183-G-A		not specified	Uncertain significance (Aug 21, 2023)
10-88913254-G-A		not specified	Uncertain significance (Jan 30, 2024)
10-88913292-G-C		not specified	Uncertain significance (Oct 03, 2023)
10-88913348-T-C		not specified	Uncertain significance (Jan 10, 2022)
10-88913351-A-G		not specified	Uncertain significance (May 18, 2022)
10-88913369-C-A		not specified	Uncertain significance (May 08, 2023)
10-88913402-A-G		not specified	Uncertain significance (Feb 22, 2023)
10-88914588-A-G		not specified	Likely benign (Jan 30, 2024)
10-88914618-T-G		not specified	Uncertain significance (Mar 01, 2024)
10-88916680-A-T		not specified	Uncertain significance (Jul 14, 2021)
10-88916773-A-C		not specified	Uncertain significance (Feb 28, 2023)
10-88916803-C-G		not specified	Uncertain significance (Sep 29, 2023)
10-88921299-C-G		not specified	Uncertain significance (Jan 31, 2024)
10-88935012-C-T			Likely benign (Jul 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STAMBPL1	protein_coding	protein_coding	ENST00000371926	10	95420

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-14	0.0430	125695	0	44	125739	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.266	221	232	0.951	0.0000117	2877
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000260	0.000260
Ashkenazi Jewish	0.00	0.00
East Asian	0.000382	0.000381
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000205	0.000193
Middle Eastern	0.000382	0.000381
South Asian	0.0000992	0.0000980
Other	0.000164	0.000163

dbNSFP

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}.
• Pathway: TGF-beta Signaling Pathway;TGF_beta_Receptor (Consensus)

Recessive Scores

• pRec: 0.0986

Intolerance Scores

• loftool: 0.731
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

• pHI: 0.127
• hipred: Y
• hipred_score: 0.601
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.688

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stambpl1

Gene ontology

• Biological process: protein deubiquitination;protein K63-linked deubiquitination
• Cellular component: endosome;cytosol;membrane
• Molecular function: thiol-dependent ubiquitin-specific protease activity;protein binding;metallopeptidase activity;metal ion binding;Lys63-specific deubiquitinase activity