SHOC2

protein-coding

SHOC2 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

NM_007373.4

Inheritance

AD

ClinVar variants

P:10U:324B:227

Top phenotype

Noonan-like syndrome with loose anagen hair 1

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr10:110,919,367-111,017,307

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~97.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cardiofaciocutaneous syndromeNO_KNOWN

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).

Noonan syndromeNO_KNOWN

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).

Costello syndromeNO_KNOWN

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).

Noonan syndrome-like disorder with loose anagen hair 1STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0054637

Submitter: PanelApp Australia

Noonan syndrome-like disorder with loose anagen hairSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011899

Submitter: Orphanet

Noonan syndrome-like disorder with loose anagen hair 1STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0054637

Submitter: Genomics England PanelApp

Noonan syndrome-like disorder with loose anagen hair 1STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0054637

Submitter: Labcorp Genetics (formerly Invitae)

Noonan syndrome-like disorder with loose anagen hair 1DEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0054637

Submitter: G2P

Noonan syndrome-like disorder with loose anagen hairDEFINITIVE

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)

Noonan-like syndrome with loose anagen hair 1AD

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

Refs: 1884862; 9301585; 12673660; 19684605Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SHOC2 variants in ClinVar

16 Conditions Cataloged
RASopathyTotal: 487
Cardiovascular phenotypeTotal: 230
not providedTotal: 102
not specifiedTotal: 59
Noonan syndrome-like disorder with loose anagen hair 1Total: 52
SHOC2-related disorderTotal: 24
Noonan syndrome and Noonan-related syndromeTotal: 21
Noonan syndromeTotal: 11

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
203
clinvar
5
clinvar
210
missense
5
clinvar
5
clinvar
310
clinvar
17
clinvar
2
clinvar
339
nonsense
3
clinvar
3
start loss
0
frameshift
6
clinvar
6
splice donor/acceptor (+/-2bp)
3
clinvar
3
Total553242207561

Highest pathogenic variant AF is 0.000006572893

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 52 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_007373.4RefSeqNP_031399.28MANE Select
ENST00000369452.9EnsemblENSP00000358464.58MANE Select
NM_001269039.3RefSeqNP_001255968.17Standard
NM_001324336.2RefSeqNP_001311265.18Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.971532970.5150.00001483803
Missense (PolyPhen)3298.6680.324321337
Synonymous0.804981090.9020.000004881139
Loss of Function4.31021.70.000.00000104331

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.00000880.0000088rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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