STAM2

signal transducing adaptor molecule 2, the group of ESCRT-0

Basic information

Region (hg38): 2:152116801-152175763

Links

ENSG00000115145 ∙ NCBI:10254 ∙ OMIM:606244 ∙ HGNC:11358 ∙ Uniprot:O75886 ∙ 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 STAM2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STAM2 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			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	28	1	0

Variants in STAM2

This is a list of pathogenic ClinVar variants found in the STAM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-152120590-T-G		not specified	Uncertain significance (Dec 06, 2023)
2-152120609-G-C		not specified	Uncertain significance (Mar 29, 2023)
2-152120691-C-T		not specified	Uncertain significance (May 25, 2022)
2-152120699-C-T		not specified	Uncertain significance (Oct 05, 2021)
2-152120707-C-T		not specified	Uncertain significance (Dec 11, 2023)
2-152120726-C-A		not specified	Uncertain significance (Aug 12, 2021)
2-152120770-T-C		not specified	Uncertain significance (Jun 30, 2022)
2-152120774-T-C		not specified	Uncertain significance (Aug 13, 2021)
2-152123916-T-C		not specified	Uncertain significance (Apr 26, 2024)
2-152126231-T-C			Likely benign (Nov 01, 2022)
2-152132120-A-G		not specified	Uncertain significance (Sep 13, 2023)
2-152132151-C-T		not specified	Uncertain significance (Oct 20, 2021)
2-152133190-T-C		not specified	Uncertain significance (Dec 01, 2022)
2-152133197-A-G		not specified	Uncertain significance (Jan 22, 2024)
2-152133444-C-A		not specified	Uncertain significance (Nov 07, 2022)
2-152133484-G-A		not specified	Uncertain significance (Jan 22, 2024)
2-152135536-T-C		not specified	Uncertain significance (May 26, 2024)
2-152135550-G-A		not specified	Uncertain significance (Mar 28, 2023)
2-152135595-T-C		not specified	Uncertain significance (Sep 17, 2021)
2-152135603-A-G		not specified	Likely benign (May 31, 2023)
2-152143907-T-A		not specified	Uncertain significance (Mar 23, 2022)
2-152143918-G-A		not specified	Uncertain significance (May 07, 2024)
2-152143954-G-C		not specified	Uncertain significance (Jul 15, 2021)
2-152144894-C-A		not specified	Uncertain significance (Sep 13, 2023)
2-152147172-G-A		not specified	Uncertain significance (Jun 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STAM2	protein_coding	protein_coding	ENST00000263904	14	59192

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000104	0.997	125676	0	72	125748	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.348	253	269	0.940	0.0000127	3444
Missense in Polyphen		70	86.922	0.80532		1138
Synonymous	0.738	84	93.1	0.903	0.00000448	975
Loss of Function	2.65	13	28.2	0.461	0.00000119	376

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000769	0.000759
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000110	0.000109
Finnish	0.000673	0.000647
European (Non-Finnish)	0.000284	0.000281
Middle Eastern	0.000110	0.000109
South Asian	0.000236	0.000229
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 (By similarity). {ECO:0000250}.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Endocytosis - Homo sapiens (human);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;TCR;Infectious disease;Fibroblast growth factor-1;EGFR downregulation;Signaling by EGFR;Clathrin-mediated endocytosis;EGFR1;Ub-specific processing proteases;IL2;Deubiquitination;IL2-mediated signaling events;Cargo recognition for clathrin-mediated endocytosis;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: 0.234

Intolerance Scores

• loftool: 0.763
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.513
• hipred: Y
• hipred_score: 0.822
• ghis: 0.651

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.810

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stam2
• Phenotype: 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); normal phenotype; immune system phenotype

Gene ontology

• Biological process: intracellular protein transport;endosomal transport;macroautophagy;multivesicular body assembly;negative regulation of epidermal growth factor receptor signaling pathway;membrane organization
• Cellular component: nucleoplasm;cytoplasm;cytosol;early endosome membrane;ESCRT-0 complex;intracellular membrane-bounded organelle
• Molecular function: protein binding