STAM

signal transducing adaptor molecule, the group of ESCRT-0

Basic information

Region (hg38): 10:17644150-17716824

Links

ENSG00000136738 ∙ NCBI:8027 ∙ OMIM:601899 ∙ HGNC:11357 ∙ Uniprot:Q92783 ∙ 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 STAM gene.

• Inborn genetic diseases (23 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STAM 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding						0
Total	0	0	22	1	0

Variants in STAM

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

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

Position	Type	Phenotype	Significance	ClinVar
10-17660539-C-G		not specified	Uncertain significance (Nov 03, 2022)
10-17660542-G-A		not specified	Uncertain significance (Jun 03, 2022)
10-17660544-A-C		not specified	Uncertain significance (Oct 05, 2023)
10-17660546-T-C			Benign (Dec 31, 2019)
10-17684733-G-A		not specified	Uncertain significance (May 15, 2023)
10-17684847-G-T		not specified	Uncertain significance (Jan 19, 2024)
10-17688058-C-G		not specified	Uncertain significance (Feb 01, 2023)
10-17693277-T-A		not specified	Uncertain significance (Mar 28, 2023)
10-17693289-A-T		not specified	Uncertain significance (Feb 15, 2023)
10-17695090-A-G		not specified	Uncertain significance (Jul 12, 2022)
10-17695140-A-C		not specified	Uncertain significance (Aug 16, 2022)
10-17695207-A-G		not specified	Uncertain significance (Nov 07, 2022)
10-17695245-A-G			Benign (Dec 01, 2022)
10-17700244-A-G		not specified	Uncertain significance (Mar 17, 2023)
10-17704465-G-A		not specified	Uncertain significance (Oct 27, 2021)
10-17704495-T-C		not specified	Uncertain significance (Mar 01, 2024)
10-17704506-C-A		not specified	Uncertain significance (Dec 06, 2021)
10-17704510-A-G		not specified	Uncertain significance (May 04, 2022)
10-17705641-T-C		not specified	Uncertain significance (Dec 16, 2023)
10-17708822-A-T		not specified	Uncertain significance (Apr 07, 2022)
10-17708840-T-G		not specified	Uncertain significance (Jun 13, 2022)
10-17708861-C-T		not specified	Uncertain significance (Dec 15, 2022)
10-17708872-T-C		not specified	Uncertain significance (Jun 30, 2023)
10-17708888-C-A		not specified	Uncertain significance (Jan 23, 2023)
10-17708900-C-T		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STAM	protein_coding	protein_coding	ENST00000377524	14	71790

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.850	0.150	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.294	279	293	0.952	0.0000147	3563
Missense in Polyphen		42	68.279	0.61513		879
Synonymous	-0.270	109	105	1.03	0.00000618	1005
Loss of Function	4.05	5	28.2	0.177	0.00000128	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in intracellular signal transduction mediated by cytokines and growth factors. Upon IL-2 and GM-CSL stimulation, it plays a role in signaling leading to DNA synthesis and MYC induction. May also play a role in T-cell development. Involved in down-regulation of receptor tyrosine kinase via multivesicular body (MVBs) when complexed with HGS (ESCRT-0 complex). The ESCRT-0 complex binds ubiquitin and acts as sorting machinery that recognizes ubiquitinated receptors and transfers them to further sequential lysosomal sorting/trafficking processes.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Endocytosis - Homo sapiens (human);JAK-STAT-Ncore;Vitamin D Receptor Pathway;VEGFA-VEGFR2 Signaling Pathway;EGF-EGFR Signaling Pathway;Disease;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Endosomal Sorting Complex Required For Transport (ESCRT);Metabolism of proteins;Infectious disease;Metalloprotease DUBs;EGFR downregulation;Signaling by EGFR;Clathrin-mediated endocytosis;EGFR1;Deubiquitination;IL2-mediated signaling events;Cargo recognition for clathrin-mediated endocytosis;IL4;IL-7;Negative regulation of MET activity;Signaling by MET;Signaling by Receptor Tyrosine Kinases;InlB-mediated entry of Listeria monocytogenes into host cell;Listeria monocytogenes entry into host cells (Consensus)

Recessive Scores

• pRec: 0.165

Intolerance Scores

• loftool: 0.398
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.65

Haploinsufficiency Scores

• pHI: 0.306
• hipred: Y
• hipred_score: 0.819
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stam
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: intracellular protein transport;signal transduction;positive regulation of signal transduction;endosomal transport;macroautophagy;protein deubiquitination;multivesicular body assembly;negative regulation of epidermal growth factor receptor signaling pathway;membrane organization;positive regulation of exosomal secretion;regulation of extracellular exosome assembly
• Cellular component: cytosol;early endosome membrane;ESCRT-0 complex
• Molecular function: SH3/SH2 adaptor activity;protein binding;ubiquitin-like protein ligase binding