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NM_015559.3(SETBP1):c.2608G>A (p.Gly870Ser) AND Schinzel-Giedion syndrome

Germline classification:
Pathogenic (4 submissions)
Last evaluated:
Dec 7, 2020
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000001090.11

Allele description

NM_015559.3(SETBP1):c.2608G>A (p.Gly870Ser)

Gene:
SETBP1:SET binding protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q12.3
Genomic location:
Preferred name:
NM_015559.3(SETBP1):c.2608G>A (p.Gly870Ser)
HGVS:
  • NC_000018.10:g.44951948G>A
  • NG_027527.2:g.276776G>A
  • NM_015559.3:c.2608G>AMANE SELECT
  • NP_056374.2:p.Gly870Ser
  • LRG_1150t1:c.2608G>A
  • LRG_1150:g.276776G>A
  • LRG_1150p1:p.Gly870Ser
  • NC_000018.9:g.42531913G>A
  • NM_015559.2:c.2608G>A
  • Q9Y6X0:p.Gly870Ser
Protein change:
G870S; GLY870SER
Links:
UniProtKB: Q9Y6X0#VAR_063809; OMIM: 611060.0005; dbSNP: rs267607040
NCBI 1000 Genomes Browser:
rs267607040
Molecular consequence:
  • NM_015559.3:c.2608G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Schinzel-Giedion syndrome (SGS)
Synonyms:
Schinzel-Giedion midface retraction syndrome
Identifiers:
MONDO: MONDO:0010010; MedGen: C0265227; Orphanet: 798; OMIM: 269150

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000021240OMIM
no assertion criteria provided
Pathogenic
(Apr 1, 2011)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV000194893Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2007)
Pathogenic
(Sep 19, 2013)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001468659HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-SouthSeq
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Dec 7, 2020)
unknownresearch

PubMed (1)
[See all records that cite this PMID]

SCV0040134773billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicunknownclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyes1not providednot provided1not providedresearch, clinical testing

Citations

PubMed

Schinzel-Giedion syndrome: report of splenopancreatic fusion and proposed diagnostic criteria.

Lehman AM, McFadden D, Pugash D, Sangha K, Gibson WT, Patel MS.

Am J Med Genet A. 2008 May 15;146A(10):1299-306. doi: 10.1002/ajmg.a.32277.

PubMed [citation]
PMID:
18398855

SETBP1 mutations in two Thai patients with Schinzel-Giedion syndrome.

Suphapeetiporn K, Srichomthong C, Shotelersuk V.

Clin Genet. 2011 Apr;79(4):391-3. doi: 10.1111/j.1399-0004.2010.01552.x. No abstract available.

PubMed [citation]
PMID:
21371013
See all PubMed Citations (7)

Details of each submission

From OMIM, SCV000021240.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

In a female child with Schinzel-Giedion syndrome (269150) who died at 9.25 years of age, Hoischen et al. (2010) identified a de novo 2608G-A transition in the SETBP1 gene, resulting in a gly870-to-ser (G870S) substitution at a highly conserved residue. The mutation was not found in the parents or in 188 control chromosomes.

In 2 unrelated Thai male infants who fulfilled the diagnostic criteria for Schinzel-Giedion syndrome proposed by Lehman et al. (2008), Suphapeetiporn et al. (2011) identified heterozygosity for the G870S mutation in the SETBP1 gene. The mutation was not found in 100 control chromosomes of Thai ethnicity. The patients displayed some features not previously reported in the disorder, including very short epiglottis, vocal cord paralysis, radioulnar synostosis, and possible hypothyroidism.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Genetic Services Laboratory, University of Chicago, SCV000194893.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology - CSER-SouthSeq, SCV001468659.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedresearch PubMed (1)

Description

ACMG codes:PS4, PM1, PM2, PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyes1not providednot provided1not providednot providednot provided

From 3billion, SCV004013477.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (4)

Description

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). The variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported. Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 23222956). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.72; 3Cnet: 0.60). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000001035 / PMID: 20436468). Different missense changes at the same codon (p.Gly870Asp, p.Gly870Cys) have been reported to be associated with SETBP1 related disorder (ClinVar ID: VCV000001034 / PMID: 20436468, 25082129). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Aug 18, 2024