SRC

protein-coding

SRC proto-oncogene, non-receptor tyrosine kinase, the group of Src family tyrosine kinases|SH2 domain containing

Gene summary

This gene is highly similar to the v-src gene of Rous sarcoma virus. This proto-oncogene may play a role in the regulation of embryonic development and cell growth. The protein encoded by this gene is a tyrosine-protein kinase whose activity can be inhibited by phosphorylation by c-SRC kinase. Mutations in this gene could be involved in the malignant progression of colon cancer. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:
  • SRC1

MANE transcript

NM_198291.3

Inheritance

AD

ClinVar variants

P:2U:65B:37

Top phenotype

Thrombocytopenia, autosomal dominant, 6

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr20:37,344,685-37,406,050

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~61.4 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

thrombocytopenia 6SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0014837

Submitter: Orphanet

thrombocytopenia 6MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0014837

Submitter: ClinGen

In 2016, the *SRC* was reported, for the first time, a disease of dominant inheritance, that presented with thrombocytopenia, myelofibrosis, bleeding, and bone pathologies in multiple members from a three-generation pedigree (Turro E, et al., 2016, PMID: 26936507). The patients carried the variant c.1579G>A (p. E527K) in the *SRC* gene, and the variant segregates with the disease phenotypes in the family (PMID: 26936507). The authors demonstrated that E527K was a gain-of-function variant, which resulted in the loss of SRC’s self-inhibitory capacity. Five additional probands have since been identified with the same variant (PMIDs: 31204551, 35349645, 33054137, 36519321, 36507135). Two were *de novo* occurrences (PMIDs: 31204551 and 33054137) and one was a Spanish family with seven patients confirmed to harbor E527K (PMID: 35349645). There is also experimental evidence to support the pathogenicity of this variant, including expression of SRC in hematopoietic cells (PMID: 2419901). Additionally, this mutation caused a defect in megakaryopoiesis from either patient cells or the normal stem cell transduced with this change (PMIDs: 26936507 and 33054137). And a Zebrafish model expressing this variant recapitulated the patient’s blood and bone phenotypes (PMID: 26936507). In summary, there is moderate evidence to support this gene-disease relationship. While more evidence is needed to establish this relationship definitively, no convincing contradictory evidence has emerged. This gene-disease pair was originally evaluated by the HT GCEP on 02/26/2020. It was reevaluated on 06/22/2022. As a result of this reevaluation, the classification remained at Moderate with the addition of new case-level evidence (PMIDs: 35349645 and 33054137). It was again reevaluated on 06/03/2024. As a result of this reevaluation, the classification remained at Moderate with the addition of new case-level evidence (PMIDs: 36519321 and 36507135).

thrombocytopenia 6STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014837

Submitter: PanelApp Australia

colorectal cancerNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005575

Submitter: Labcorp Genetics (formerly Invitae)

thrombocytopenia 6LIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0014837

Submitter: Labcorp Genetics (formerly Invitae)

Clinical Genomic Database (CGD)

Thrombocytopenia, autosomal dominant, 6AD

Manifestation: Hematologic; Musculoskeletal

Intervention: Hematologic

Rationale: Individuals have been described with bleeding diathesis, including after dental/surgical procedures, and awareness may allow preventive measures and prompt treatment

Refs: 26936507Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SRC variants in ClinVar

9 Conditions Cataloged
not specifiedTotal: 81
not providedTotal: 41
SRC-related disorderTotal: 25
Thrombocytopenia 6Total: 4
ThrombocytopeniaTotal: 1
Primary myelofibrosisTotal: 1
OsteoporosisTotal: 1
Intellectual disability, autosomal dominant 40Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198291.3. 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.

EffectPLPVUSLBBSum
synonymous
8
clinvar
35
clinvar
1
clinvar
44
missense
1
clinvar
52
clinvar
1
clinvar
54
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total1165361104

Highest pathogenic variant AF is 6.876737e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 68 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_198291.3RefSeqNP_938033.111MANE Select
ENST00000373578.7EnsemblENSP00000362680.211MANE Select
NM_005417.5RefSeqNP_005408.111Standard
ENST00000358208.10EnsemblENSP00000350941.513Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
srcDanio rerio

Structure: ceratobranchial cartilage

Quality: morphology

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Inflammatory mediator regulation of TRP channels - Homo sapiens (human)
  • Platelet activation - Homo sapiens (human)
  • Focal adhesion - Homo sapiens (human)
  • Relaxin signaling pathway - Homo sapiens (human)
  • Oxytocin signaling pathway - Homo sapiens (human)

Biological Process

  • primary ovarian follicle growth
  • stimulatory C-type lectin receptor signaling pathway
  • cell cycle
  • signal transduction
  • transmembrane receptor protein tyrosine kinase signaling pathway

Molecular Function

  • protein kinase activity
  • protein tyrosine kinase activity
  • non-membrane spanning protein tyrosine kinase activity
  • SH3/SH2 adaptor activity
  • protein kinase C binding

Cellular Component

  • podosome
  • nucleus
  • cytoplasm
  • mitochondrion
  • mitochondrial inner membrane

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000373578
Coding exons
11
Length
61366
Individuals with no LoFs
125652
Homozygous LoFs
0
Heterozygous LoFs
2
Defined
125654
p
0.00000796
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.871293260.3960.00002093405
Missense (PolyPhen)48181.220.264871831
Synonymous0.8661351480.9100.00001041076
Loss of Function4.34225.80.07750.00000120306

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.00000900.0000088rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Non-receptor protein tyrosine kinase which is activated following engagement of many different classes of cellular receptors including immune response receptors, integrins and other adhesion receptors, receptor protein tyrosine kinases, G protein- coupled receptors as well as cytokine receptors. Participates in signaling pathways that control a diverse spectrum of biological activities including gene transcription, immune response, cell adhesion, cell cycle progression, apoptosis, migration, and transformation. Due to functional redundancy between members of the SRC kinase family, identification of the specific role of each SRC kinase is very difficult. SRC appears to be one of the primary kinases activated following engagement of receptors and plays a role in the activation of other protein tyrosine kinase (PTK) families. Receptor clustering or dimerization leads to recruitment of SRC to the receptor complexes where it phosphorylates the tyrosine residues within the receptor cytoplasmic domains. Plays an important role in the regulation of cytoskeletal organization through phosphorylation of specific substrates such as AFAP1. Phosphorylation of AFAP1 allows the SRC SH2 domain to bind AFAP1 and to localize to actin filaments. Cytoskeletal reorganization is also controlled through the phosphorylation of cortactin (CTTN) (Probable). When cells adhere via focal adhesions to the extracellular matrix, signals are transmitted by integrins into the cell resulting in tyrosine phosphorylation of a number of focal adhesion proteins, including PTK2/FAK1 and paxillin (PXN) (PubMed:21411625). In addition to phosphorylating focal adhesion proteins, SRC is also active at the sites of cell-cell contact adherens junctions and phosphorylates substrates such as beta- catenin (CTNNB1), delta-catenin (CTNND1), and plakoglobin (JUP). Another type of cell-cell junction, the gap junction, is also a target for SRC, which phosphorylates connexin-43 (GJA1). SRC is implicated in regulation of pre-mRNA-processing and phosphorylates RNA-binding proteins such as KHDRBS1 (Probable). Also plays a role in PDGF-mediated tyrosine phosphorylation of both STAT1 and STAT3, leading to increased DNA binding activity of these transcription factors (By similarity). Involved in the RAS pathway through phosphorylation of RASA1 and RASGRF1 (PubMed:11389730). Plays a role in EGF-mediated calcium-activated chloride channel activation (PubMed:18586953). Required for epidermal growth factor receptor (EGFR) internalization through phosphorylation of clathrin heavy chain (CLTC and CLTCL1) at 'Tyr-1477'. Involved in beta-arrestin (ARRB1 and ARRB2) desensitization through phosphorylation and activation of GRK2, leading to beta-arrestin phosphorylation and internalization. Has a critical role in the stimulation of the CDK20/MAPK3 mitogen-activated protein kinase cascade by epidermal growth factor (Probable). Might be involved not only in mediating the transduction of mitogenic signals at the level of the plasma membrane but also in controlling progression through the cell cycle via interaction with regulatory proteins in the nucleus (PubMed:7853507). Plays an important role in osteoclastic bone resorption in conjunction with PTK2B/PYK2. Both the formation of a SRC-PTK2B/PYK2 complex and SRC kinase activity are necessary for this function. Recruited to activated integrins by PTK2B/PYK2, thereby phosphorylating CBL, which in turn induces the activation and recruitment of phosphatidylinositol 3-kinase to the cell membrane in a signaling pathway that is critical for osteoclast function (PubMed:8755529, PubMed:14585963). Promotes energy production in osteoclasts by activating mitochondrial cytochrome C oxidase (PubMed:12615910). Phosphorylates DDR2 on tyrosine residues, thereby promoting its subsequent autophosphorylation (PubMed:16186108). Phosphorylates RUNX3 and COX2 on tyrosine residues, TNK2 on 'Tyr-284' and CBL on 'Tyr-731' (PubMed:20100835, PubMed:21309750). Enhances DDX58/RIG-I-elicited antiviral signaling (PubMed:19419966). Phosphorylates PDPK1 at 'Tyr-9', 'Tyr-373' and 'Tyr-376' (PubMed:14585963). Phosphorylates BCAR1 at 'Tyr-128' (PubMed:22710723). Phosphorylates CBLC at multiple tyrosine residues, phosphorylation at 'Tyr-341' activates CBLC E3 activity (PubMed:20525694). Involved in anchorage-independent cell growth (PubMed:19307596). Required for podosome formation (By similarity). {ECO:0000250|UniProtKB:P05480, ECO:0000269|PubMed:11389730, ECO:0000269|PubMed:12615910, ECO:0000269|PubMed:14585963, ECO:0000269|PubMed:16186108, ECO:0000269|PubMed:18586953, ECO:0000269|PubMed:19307596, ECO:0000269|PubMed:19419966, ECO:0000269|PubMed:20100835, ECO:0000269|PubMed:20525694, ECO:0000269|PubMed:21309750, ECO:0000269|PubMed:21411625, ECO:0000269|PubMed:22710723, ECO:0000269|PubMed:7853507, ECO:0000269|PubMed:8755529, ECO:0000269|PubMed:8759729, ECO:0000305|PubMed:11964124, ECO:0000305|PubMed:8672527, ECO:0000305|PubMed:9442882}.;
Disease
DISEASE: Note=SRC kinase activity has been shown to be increased in several tumor tissues and tumor cell lines such as colon carcinoma cells. {ECO:0000269|PubMed:2498394, ECO:0000269|PubMed:3093483}.; DISEASE: Thrombocytopenia 6 (THC6) [MIM:616937]: A form of thrombocytopenia, a hematologic disorder defined by a decrease in the number of platelets in circulating blood, resulting in the potential for increased bleeding and decreased ability for clotting. THC6 is an autosomal dominant form. Affected individuals may also have bone abnormalities and an increased risk for myelofibrosis. {ECO:0000269|PubMed:26936507}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.995

Intolerance Scores

LoFtool
0.0217
RVIS EVS
-0.69
RVIS percentile EVS
14.97

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Indispensability pred.
E
Indispensability score
0.935

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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