STAP2

protein-coding

signal transducing adaptor family member 2

Gene summary

This gene encodes the substrate of breast tumor kinase, an Src-type non-receptor tyrosine kinase. The encoded protein possesses domains and several tyrosine phosphorylation sites characteristic of adaptor proteins that mediate the interactions linking proteins involved in signal transduction pathways. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001013841.2

Inheritance

—

ClinVar variants

U:83B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.02

Max pathogenic AF

—

Genomic locus

chr19:4,324,043-4,342,786

External References & Databases

Ensembl (ENSG00000178078)

Transcript & Mutation Effects

hg38 • Region Span ~18.7 kb

Loading mutation effect viewer...

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 STAP2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 83

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001013841.2. 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			3 clinvar			3
missense			76 clinvar	5 clinvar		81
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	83	5	0	88

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 79 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001013841.2	RefSeq	NP_001013863.1	13	MANE Select
ENST00000594605.6	Ensembl	ENSP00000471052.1	13	MANE Select
NM_017720.3	RefSeq	NP_060190.2	13	Standard
ENST00000598443.5	Ensembl	ENSP00000471281.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by PTK6
Signal Transduction
PTK6 Activates STAT3
Signaling by Non-Receptor Tyrosine Kinases

Biological Process

positive regulation of tyrosine phosphorylation of STAT protein

Molecular Function

protein binding
signaling adaptor activity

Cellular Component

cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000600324
Coding exons: 13
Length: 18744
Individuals with no LoFs: 123464
Homozygous LoFs: 18
Heterozygous LoFs: 2266
Defined: 125748
p: 0.00912

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.598	235	262	0.896	0.0000145	2856
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0026	0.0024	notable
Latino/Admixed American	0.0045	0.0045	notable
Ashkenazi Jewish	0.00061	0.00060	rare
East Asian	0.000055	0.000054	rare
Finnish	0.0087	0.0081	notable
European (Non-Finnish)	0.017	0.016	notable
South Asian	0.0030	0.0029	notable
Other	0.0083	0.0080	notable

dbNSFP Gene Annotations

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}.;

Intolerance Scores

LoFtool: 0.976
RVIS EVS: -0.44
RVIS percentile EVS: 24.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.349

Gene Damage Prediction

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