rs267607040

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PM5PP3_ModeratePP5_Very_Strong

The NM_015559.3(SETBP1):​c.2608G>A​(p.Gly870Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,882 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G870R) has been classified as Likely pathogenic.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

SETBP1
NM_015559.3 missense

Scores

13
4
2

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:11

Conservation

PhyloP100: 9.97
Variant links:
Genes affected
SETBP1 (HGNC:15573): (SET binding protein 1) This gene encodes a protein which contains a several motifs including a ski homology region and a SET-binding region in addition to three nuclear localization signals. The encoded protein has been shown to bind the SET nuclear oncogene which is involved in DNA replication. Mutations in this gene are associated with Schinzel-Giedion midface retraction syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 16 ACMG points.

PM1
In a compositionally_biased_region Polar residues (size 28) in uniprot entity SETBP_HUMAN there are 13 pathogenic changes around while only 0 benign (100%) in NM_015559.3
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chrnull-null-null-null is described in UniProt as null.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.859
PP5
Variant 18-44951948-G-A is Pathogenic according to our data. Variant chr18-44951948-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 1035.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr18-44951948-G-A is described in Lovd as [Pathogenic]. Variant chr18-44951948-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SETBP1NM_015559.3 linkuse as main transcriptc.2608G>A p.Gly870Ser missense_variant 4/6 ENST00000649279.2 NP_056374.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SETBP1ENST00000649279.2 linkuse as main transcriptc.2608G>A p.Gly870Ser missense_variant 4/6 NM_015559.3 ENSP00000497406 P2Q9Y6X0-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000205
AC:
3
AN:
1461882
Hom.:
0
Cov.:
38
AF XY:
0.00000413
AC XY:
3
AN XY:
727244
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000270
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00152
Hom.:
0
ExAC
AF:
0.0000165
AC:
2

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:11
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Schinzel-Giedion syndrome Pathogenic:6
Pathogenic, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoSep 19, 2013- -
Pathogenic, criteria provided, single submitterclinical testingKasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India-In-silico analysis tools (REVEL, CADD, and FATHMM) predict the variant to be disease-causing and affect the SETBP1 protein function. Heterozygous variants in SETBP1 are associated with the intellectual developmental disorder, autosomal dominant 29 (MIM# 616078) and Schinzel-Giedion midface retraction syndrome (MIM# 269150). The above-mentioned variant is a recurrent variant in individuals with Schinzel-Giedion midface retraction syndrome (Hoischen et al.,2010). Also, this variant was reported in the ClinVar database as a pathogenic variant in nine independent submissions (variation id. 1035). -
Pathogenic, criteria provided, single submitterclinical testingRoyal Medical Services, Bahrain Defence Force Hospital-The SETBP1 variant c.2608G>A p.(Gly870Ser) causes an amino acid change from Gly to Ser at position 870. According to HGMD Professional 2022.1, this variant has previously been described as disease causing for Schinzel-Giedion syndrome by Hoischen et al., 2010 (PMID: 20436468), Suphapeetiporn et al., 2011 (PMID: 21371013), Ko et al., 2013 (PMID: 23400866). ClinVar lists this variant (Interpretation: Pathogenic; Variation ID: 1035). It is classified as pathogenic (class 1) according to the recommendations of CENTOGENE and ACMG. -
Pathogenic, criteria provided, single submitterclinical testing3billion-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. -
Pathogenic, no assertion criteria providedliterature onlyOMIMApr 01, 2011- -
Pathogenic, criteria provided, single submitterresearchHudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for BiotechnologyDec 07, 2020ACMG codes:PS4, PM1, PM2, PP3 -
not provided Pathogenic:3
Pathogenic, criteria provided, single submitterclinical testingGeneDxJul 17, 2023Published functional studies demonstrate a damaging effect (significant increase in cell proliferation) (Piazza et al., 2013); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 20436468, 26188272, 21371013, 23400866, 29333303, 32460883, 18398855, Neupauerova2019[casereport], 28209656, 28881700, 28419882, 31692115, 33822276, 29549983, 29435294, 28346496, 23222956) -
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMar 11, 2022Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SETBP1 protein function. ClinVar contains an entry for this variant (Variation ID: 1035). This missense change has been observed in individual(s) with Schinzel-Giedion syndrome (PMID: 20436468, 21371013). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 870 of the SETBP1 protein (p.Gly870Ser). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitterclinical testingRevvity Omics, RevvityFeb 09, 2021- -
SETBP1-related disorder Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesAug 30, 2022The SETBP1 c.2608G>A variant is predicted to result in the amino acid substitution p.Gly870Ser. This variant has been well-documented to be pathogenic for Schinzel-Giedion syndrome (Hoischen et al. 2010. PubMed ID: 20436468; Acuna-Hidalgo et al. 2017. PubMed ID: 28346496. Table S1 and S4). This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/18-42531913-G-A). This variant is interpreted as pathogenic. -
Pathogenic, criteria provided, single submitterclinical testingRady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego-The c.2608G>A (p.Gly870Ser) variant affects a highly conserved amino acid; however, in silico tools used to predict the effect of this variant on protein function yield discordant results. This variant has been previously reported as a de novo and heterozygous change in patients with Schinzel-Giedion syndrome (PMID: 20436468, 21371013, 23400866, 26188272, 28346496, 29333303, 32460883, 23222956). Functional studies indicate this variant may lead to higher amounts of SETBP1 protein (PMID: 23222956). The c.2608G>A (p.Gly870Ser) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.0003% (1/251064). The sequence data provided for the gnomAD entry shows the c.2608G>A (p.Gly870Ser) in only 12% of NGS reads in an individual reported to be over the age of 75, therefore, the gnomAD entry likely represents an age-related somatic event (PMID: 23222956, 23832012). Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, c.2608G>A (p.Gly870Ser) is classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
1.0
BayesDel_addAF
Pathogenic
0.44
D
BayesDel_noAF
Pathogenic
0.40
CADD
Pathogenic
29
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.75
D;D
Eigen
Pathogenic
0.84
Eigen_PC
Pathogenic
0.88
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Pathogenic
0.98
.;D
M_CAP
Uncertain
0.10
D
MetaRNN
Pathogenic
0.86
D;D
MetaSVM
Uncertain
0.68
D
MutationAssessor
Benign
2.0
M;M
MutationTaster
Benign
1.0
D
PrimateAI
Pathogenic
0.93
D
PROVEAN
Pathogenic
-5.7
.;D
REVEL
Pathogenic
0.72
Sift
Pathogenic
0.0
.;D
Sift4G
Pathogenic
0.0
.;D
Polyphen
1.0
D;D
Vest4
0.98
MutPred
0.31
Gain of glycosylation at G870 (P = 0.0113);Gain of glycosylation at G870 (P = 0.0113);
MVP
0.97
MPC
0.91
ClinPred
1.0
D
GERP RS
6.2
Varity_R
0.93
gMVP
0.64

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs267607040; hg19: chr18-42531913; COSMIC: COSV56311834; API