NM_015559.3(SETBP1):c.2601C>A (p.Ser867Arg) AND Schinzel-Giedion syndrome

Germline classification:: Likely pathogenic (1 submission)
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002510727.2

Allele description [Variation Report for NM_015559.3(SETBP1):c.2601C>A (p.Ser867Arg)]

NM_015559.3(SETBP1):c.2601C>A (p.Ser867Arg)

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.2601C>A (p.Ser867Arg)

HGVS:

NC_000018.10:g.44951941C>A
NG_027527.2:g.276769C>A
NM_001379141.1:c.2601C>A
NM_001379142.1:c.2601C>A
NM_001410862.1:c.2601C>A
NM_015559.3:c.2601C>AMANE SELECT
NP_001366070.1:p.Ser867Arg
NP_001366071.1:p.Ser867Arg
NP_001397791.1:p.Ser867Arg
NP_056374.2:p.Ser867Arg
LRG_1150t1:c.2601C>A
LRG_1150:g.276769C>A
LRG_1150p1:p.Ser867Arg
NC_000018.9:g.42531906C>A
NM_015559.2:c.2601C>A

Protein change:

S867R

Molecular consequence:

NM_001379141.1:c.2601C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001379142.1:c.2601C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001410862.1:c.2601C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_015559.3:c.2601C>A - missense variant - [Sequence Ontology: SO:0001583]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002820273	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002820273

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV002820273.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The missense variant p.S867R in SETBP1 (NM_015559.2) has been reported previously as a de novo mutation in two separate individuals with Schinzel Giedion syndrome (Acuna-Hidalgo et al, Carvalho E et al). Described children had seizures, psychomotor delay and dysmorphism with or without congenital malformations. The p.S867R variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. There is a moderate physicochemical difference between serine and arginine. The variant in present just adjacent to the 12bp hotspot region in SETBP1 gene. For these reasons, this variant has been classified as Likely Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 6, 2024

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