NM_015559.3(SETBP1):c.2665C>T (p.Arg889Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 16, 2023
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:: RCV003768469.1

Allele description [Variation Report for NM_015559.3(SETBP1):c.2665C>T (p.Arg889Ter)]

NM_015559.3(SETBP1):c.2665C>T (p.Arg889Ter)

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.2665C>T (p.Arg889Ter)

HGVS:

NC_000018.10:g.44952005C>T
NG_027527.2:g.276833C>T
NM_015559.3:c.2665C>TMANE SELECT
NP_056374.2:p.Arg889Ter
LRG_1150t1:c.2665C>T
LRG_1150:g.276833C>T
LRG_1150p1:p.Arg889Ter
NC_000018.9:g.42531970C>T

Protein change:

R889*

Links:

dbSNP: rs1599368734

NCBI 1000 Genomes Browser:

rs1599368734

Molecular consequence:

NM_015559.3:c.2665C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004640891	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 16, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 21037274, 25217958, 32345733, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004640891

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 16, 2023)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel-Giedion syndrome.

Filges I, Shimojima K, Okamoto N, Röthlisberger B, Weber P, Huber AR, Nishizawa T, Datta AN, Miny P, Yamamoto T.

J Med Genet. 2011 Feb;48(2):117-22. doi: 10.1136/jmg.2010.084582. Epub 2010 Oct 30.

PubMed [citation]

PMID:: 21037274

Refining analyses of copy number variation identifies specific genes associated with developmental delay.

Coe BP, Witherspoon K, Rosenfeld JA, van Bon BW, Vulto-van Silfhout AT, Bosco P, Friend KL, Baker C, Buono S, Vissers LE, Schuurs-Hoeijmakers JH, Hoischen A, Pfundt R, Krumm N, Carvill GL, Li D, Amaral D, Brown N, Lockhart PJ, Scheffer IE, Alberti A, Shaw M, et al.

Nat Genet. 2014 Oct;46(10):1063-71. doi: 10.1038/ng.3092. Epub 2014 Sep 14.

PubMed [citation]

PMID:: 25217958
PMCID:: PMC4177294

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004640891.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Arg889*) in the SETBP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SETBP1 are known to be pathogenic (PMID: 21037274, 25217958). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with SETBP1-related conditions (PMID: 32345733). ClinVar contains an entry for this variant (Variation ID: 636309). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: May 7, 2024

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