STAP2

signal transducing adaptor family member 2

Basic information

Region (hg38): 19:4324043-4342786

Links

ENSG00000178078 ∙ NCBI:55620 ∙ OMIM:607881 ∙ HGNC:30430 ∙ Uniprot:Q9UGK3 ∙ 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 STAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STAP2 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			36	3		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3	3		6
Total	0	0	39	6	0

Variants in STAP2

This is a list of pathogenic ClinVar variants found in the STAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4324150-G-A		not specified	Uncertain significance (Mar 18, 2024)
19-4324194-A-G		not specified	Uncertain significance (Dec 01, 2022)
19-4324527-G-A		not specified	Uncertain significance (Jan 03, 2024)
19-4324572-C-A		not specified	Uncertain significance (Nov 18, 2022)
19-4324573-G-T			Likely benign (Oct 01, 2023)
19-4324597-T-C			Likely benign (Oct 01, 2023)
19-4324605-G-A		not specified	Uncertain significance (Nov 15, 2021)
19-4324629-C-T		not specified	Uncertain significance (May 24, 2023)
19-4324632-G-T		not specified	Likely benign (Oct 10, 2023)
19-4325290-G-A		not specified	Uncertain significance (Aug 02, 2023)
19-4325300-A-C		not specified	Uncertain significance (Nov 14, 2023)
19-4325441-T-C		not specified	Uncertain significance (Nov 18, 2022)
19-4325444-C-T		not specified	Uncertain significance (Feb 28, 2023)
19-4325503-G-A		not specified	Likely benign (Jan 03, 2024)
19-4325530-G-A		not specified	Uncertain significance (Mar 06, 2025)
19-4326945-G-A		not specified	Uncertain significance (Nov 13, 2024)
19-4326951-G-C		not specified	Uncertain significance (Sep 01, 2021)
19-4326974-T-G		not specified	Uncertain significance (Jul 08, 2022)
19-4326989-T-C		not specified	Uncertain significance (Oct 12, 2021)
19-4327007-C-G		not specified	Uncertain significance (Jan 23, 2025)
19-4327140-G-C		not specified	Uncertain significance (Dec 03, 2024)
19-4327145-C-T		not specified	Uncertain significance (Sep 25, 2024)
19-4327177-G-A		not specified	Uncertain significance (Dec 12, 2023)
19-4327180-T-C		not specified	Uncertain significance (Aug 26, 2024)
19-4327180-T-G		not specified	Uncertain significance (Sep 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STAP2	protein_coding	protein_coding	ENST00000600324	13	18744

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.63e-16	0.00668	123464	18	2266	125748	0.00912

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.598	235	262	0.896	0.0000145	2856
Missense in Polyphen		61	69.792	0.87402		759
Synonymous	0.308	104	108	0.962	0.00000599	904
Loss of Function	-0.0828	24	23.6	1.02	0.00000110	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00710	0.00694
Ashkenazi Jewish	0.000611	0.000595
East Asian	0.0000553	0.0000544
Finnish	0.00871	0.00812
European (Non-Finnish)	0.0165	0.0157
Middle Eastern	0.0000553	0.0000544
South Asian	0.00303	0.00294
Other	0.00829	0.00801

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate of protein kinase PTK6. May play a regulatory role in the acute-phase response in systemic inflammation and may modulate STAT3 activity. {ECO:0000269|PubMed:10980601}.
• Pathway: Signaling by PTK6;Signal Transduction;PTK6 Activates STAT3;Signaling by Non-Receptor Tyrosine Kinases (Consensus)

Intolerance Scores

• loftool: 0.976
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.146
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.349

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Stap2
• Phenotype: normal phenotype

Gene ontology

• Biological process: positive regulation of tyrosine phosphorylation of STAT protein
• Cellular component: cytosol;plasma membrane
• Molecular function: protein binding;signaling adaptor activity