SHOC2
protein-codingSHOC2 leucine rich repeat scaffold protein, the group of MicroRNA protein coding host genes
Gene summary
This gene encodes a protein that consists almost entirely of leucine-rich repeats, a domain implicated in protein-protein interactions. The protein may function as a scaffold linking RAS to downstream signal transducers in the RAS/ERK MAP kinase signaling cascade. Mutations in this gene have been associated with Noonan-like syndrome with loose anagen hair. [provided by RefSeq, May 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~97.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0015280
Submitter: ClinGen
Two publications have identified patients with typical features of cardiofaciocutaneous syndrome (CFC) and the p.Ser2Gly variant occuring in de novo cases and cases of unknown variant origin (Lee 2011, Komatsuzaki 2015). However, all of the individuals identified were also described to have loose anagen hair (LAH); therefore, these cases should all be considered SHOC2-Noonan syndrome-like disorder with LAH (NS/LAH) patients. The p.Ser2Gly variant has been a recurrently identified variant in cases with NS/LAH, and no other variants have been identified in these patients (Cordeddu et al., 2009; Ekvall et al., 2011; Komatsuzaki et al., 2010). In summary, this association is Disputed. Of note, SHOC2 is classified as Definitive in association with NS/LAH and as Disputed in association with NS and Costello syndrome. The ClinGen RASopathy Expert Panel found no evidence associating SHOC2 with NS with multiple lentigines. This curation was approved by the ClinGen RASopathy Gene Curation Expert Panel on 6/1/18 (SOP Version 5).
Inheritance Pattern: AD
Disease ID:MONDO:0018997
Submitter: ClinGen
There have been cases described in the literature with the p.Ser2Gly variant in SHOC2 who were diagnosed with Noonan syndrome (NS) but were not phenotyped for loose anagen hair (LAH) (Hoban, Roberts, Demmer, Jethva, & Shephard, 2012; Justino et al., 2015; Komatsuzaki et al., 2010). There has only been one NS case where LAH was assessed but not noted, and this individual had sparse and curly hair. Therefore, the NS/LAH phenotype cannot be ruled out for any of these patients. The p.Ser2Gly variant has been a recurrently identified variant in cases with NS/LAH, and no other variants have been identified in these patients (Cordeddu et al., 2009; Ekvall et al., 2011; Komatsuzaki et al., 2010). In summary, this association is Disputed. Of note, SHOC2 is classified as Definitive in association with NS-like disorder with loose anagen hair and as Disputed in association with Costello syndrome and cardiofaciocutaneous syndrome. The ClinGen RASopathy Expert Panel found no evidence associating SHOC2 with NS with multiple lentigines. This curation was approved by the ClinGen RASopathy Gene Curation Expert Panel on 5/31/18 (SOP Version 5).
Inheritance Pattern: AD
Disease ID:MONDO:0009026
Submitter: ClinGen
There have been 2 published cases that were initially diagnosed with suspected Costello syndrome (Komatsuzaki et al., 2010) and the p.S2G variant. However, these individuals also presented with hair anomalies consistent with loose anagen hair, therefore it was concluded both in the paper and by the RASopathy Expert Panel that these cases are more consistent with Noonan-like syndrome with loose anagen hair (NS/LAH). The p.S2G variant has been recurrently identified in cases with NS/LAH (Cordeddu et al., 2009; Ekvall, Hagenas, Allanson, Anneren, & Bondeson, 2011; Komatsuzaki et al., 2010). This association is Disputed. The HRAS gene is believed to be the only gene associated with CS (Aoki et al., 2005; Estep, Tidyman, Teitell, Cotter, & Rauen, 2006; Gripp et al., 2006; Kerr et al., 2006; Zampino et al., 2007). Of note, SHOC2 is classified as Definitive in association with NS/LAH and as Disputed in association with NS and cardiofaciocutaneous syndrome. The ClinGen RASopathy Expert Panel found no evidence associating SHOC2 with NS with multiple lentigines. This curation was approved by the ClinGen RASopathy Gene Curation Expert Panel on 7/24/18 (SOP Version 5).
Inheritance Pattern: AD
Disease ID:MONDO:0054637
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0011899
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0054637
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0054637
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0054637
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0011899
Submitter: ClinGen
There is a definitive association between alteration of the SHOC2 gene and Noonan syndrome with loose anagen hair (NS/LAH). The maximum amount of scorable genetic evidence has been published showing the de novo p.Ser2Gly variant occurs in SHOC2 in patients with NS/LAH (Cordeddu et al., 2009; Galperin, Abdelmoti, & Sorkin, 2012; Motta et al., 2016). Additionally, the p.Met173Ile variant has been identified in one family with disease (Hannig, Jeoung, Jang, Phillips, & Galperin, 2014). The SHOC2 gene is also associated with the Ras/MAPK pathway, which is associated with the NS/LAH phenotype and variants found in NS/LAH patients in this gene disrupt the RAS pathway function as demonstrated by C. elegans models (Cordeddu et al., 2009; Gripp et al., 2016). Of note, SHOC2 is also classified as Disputed in association with NS, cardiofaciocutaneous syndrome, and Costello syndrome. The ClinGen RASopathy Expert Panel found no evidence associating SHOC2 with NS with multiple lentigines. This curation was approved by the ClinGen RASopathy Gene Curation Expert Panel on 7/25/18 (SOP Version 5).
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Dermatologic; Endocrine; Hematologic; Musculoskeletal; Neurologic
Intervention: Cardiovascular; Endocrine; Hematologic
Rationale: Surveillance and treatment related to manifestations such as cardiac anomalies (which include pulmonic stenosis and hypertrophic cardiomyopathy) can be beneficial; Recognition of endocrine anomalies (eg, GH deficiency) may allow early diagnosis and treatment; Individuals with coagulopathy have been reported, and awareness may allow prompt recognition and management
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SHOC2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_007373.4. 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 | 2 | 203 | 5 | 210 | ||
| missense | 5 | 5 | 310 | 17 | 2 | 339 |
| nonsense | 3 | 3 | ||||
| start loss | 0 | |||||
| frameshift | 6 | 6 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 5 | 5 | 324 | 220 | 7 | 561 |
Highest pathogenic variant AF is 0.000006572893
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_031399.2 | 8 | MANE Select | |
| Ensembl | ENSP00000358464.5 | 8 | MANE Select | |
| RefSeq | NP_001255968.1 | 7 | Standard | |
| RefSeq | NP_001311265.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Ras signaling pathway - Homo sapiens (human)
- EGF-Ncore
- miR-targeted genes in leukocytes - TarBase
- miR-targeted genes in lymphocytes - TarBase
- miR-targeted genes in muscle cell - TarBase
Biological Process
- protein dephosphorylation
- Ras protein signal transduction
- fibroblast growth factor receptor signaling pathway
- regulation of phosphoprotein phosphatase activity
- positive regulation of Ras protein signal transduction
Molecular Function
- protein serine/threonine phosphatase activity
- protein binding
- protein phosphatase 1 binding
- protein phosphatase regulator activity
- protein phosphatase binding
Cellular Component
- protein phosphatase type 1 complex
- photoreceptor inner segment
- nucleus
- nucleoplasm
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000369452
- Coding exons
- 8
- Length
- 94125
- Individuals with no LoFs
- 125674
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 125675
- p
- 0.00000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.97 | 153 | 297 | 0.515 | 0.0000148 | 3803 |
| Missense (PolyPhen) | 32 | 98.668 | 0.32432 | 1337 | ||
| Synonymous | 0.804 | 98 | 109 | 0.902 | 0.00000488 | 1139 |
| Loss of Function | 4.31 | 0 | 21.7 | 0.00 | 0.00000104 | 331 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulatory subunit of protein phosphatase 1 (PP1c) that acts as a M-Ras/MRAS effector and participates in MAPK pathway activation. Upon M-Ras/MRAS activation, targets PP1c to specifically dephosphorylate the 'Ser-259' inhibitory site of RAF1 kinase and stimulate RAF1 activity at specialized signaling complexes. {ECO:0000269|PubMed:10783161, ECO:0000269|PubMed:16630891, ECO:0000269|PubMed:25137548}.;
- Disease
- DISEASE: Noonan syndrome-like disorder with loose anagen hair 1 (NSLH1) [MIM:607721]: A syndrome characterized by Noonan dysmorphic features such as macrocephaly, high forehead, hypertelorism, palpebral ptosis, low-set and posteriorly rotated ears, short and webbed neck, pectus anomalies, in association with pluckable, sparse, thin and slow-growing hair. {ECO:0000269|PubMed:19684605, ECO:0000269|PubMed:23918763, ECO:0000269|PubMed:25137548}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.246
Intolerance Scores
- LoFtool
- 0.0544
- RVIS EVS
- -0.18
- RVIS percentile EVS
- 39.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.984
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |