rs797045277
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PP3_StrongPP5_Very_Strong
The NM_001374828.1(ARID1B):c.4479G>A(p.Pro1493=) variant causes a splice region, synonymous change involving the alteration of a conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. P1493P) has been classified as Pathogenic.
Frequency
Consequence
NM_001374828.1 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID1B | NM_001374828.1 | c.4479G>A | p.Pro1493= | splice_region_variant, synonymous_variant | 17/20 | ENST00000636930.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID1B | ENST00000636930.2 | c.4479G>A | p.Pro1493= | splice_region_variant, synonymous_variant | 17/20 | 2 | NM_001374828.1 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 1445994Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 717232
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Coffin-Siris syndrome 1 Pathogenic:7
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 22, 2014 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 09, 2012 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Knight Diagnostic Laboratories, Oregon Health and Sciences University | Aug 27, 2019 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | May 05, 2020 | This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. [PMID 22405089, 27474218, 29286531, 28323383] - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Pathogenic, criteria provided, single submitter | research | HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology | Jan 12, 2017 | - - |
See cases Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University Hospital Muenster | Dec 10, 2021 | ACMG categories: PS5,PM2,PP3 - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli | Apr 26, 2021 | PVS1_strong;PM2_supporting;PM6_moderate - |
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 17, 2022 | This variant has been observed in individual(s) with clinical features of Coffin-Siris syndrome and/or Coffin-Siris syndrome (PMID: 22405089, 27474218, 28323383). 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 affects codon 1370 of the ARID1B mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the ARID1B protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. ClinVar contains an entry for this variant (Variation ID: 210291). For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 17 and introduces a premature termination codon (PMID: 22405089). The resulting mRNA is expected to undergo nonsense-mediated decay. - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Sep 07, 2022 | Affects the splice donor site and induces skipping of exon 17 causing a frameshift leading to a premature Stop codon (p.Arg1338ArgfsX76) (Hoyer et al., 2012); Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 30349098, 22405089, 28323383, 27474218, 29286531, 15057123, 31406558) - |
ARID1B-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 20, 2023 | The ARID1B c.4110G>A variant is not predicted to result in an amino acid change (p.=). This variant is predicted to weaken the canonical splice donor site (Alamut Visual Plus v1.6.1). This variant has been reported in multiple individuals with Coffin-Siris syndrome and the majority of cases were found to be de novo (see for example, Hoyer et al. 2012. PubMed ID: 22405089; Mignot et al. 2016. PubMed ID: 27474218; Tumienė et al. 2018. PubMed ID: 29286531; van der Sluijs et al. 2019. PubMed ID: 30349098). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating it is rare or absent in the general population. cDNA analyses indicated that this variant causes skipping of exon 17 and a shift to the translation reading frame (p.Arg1338Argfs*76, Hoyer et al. 2012. PubMed ID: 22405089) This variant is interpreted as pathogenic. - |
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 12, 2024 | The c.4110G>A (p.P1370P) alteration is located in coding exon 17 of the ARID1B gene. This nucleotide substitution does not change the proline (P) at codon 1370. However, this change occurs in the last base pair of coding exon 17, which makes it likely to have some effect on normal mRNA splicing. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This alteration has been reported as a de novo occurrence in multiple unrelated individuals with CSS (Hoyer, 2012; Mignot, 2016; Zweier, 2017). This nucleotide position is highly conserved in available vertebrate species. RNA functional analysis demonstrated that the alteration leads to out-of-frame skipping of exon 17 (Hoyer, 2012). In silico splice site analysis predicts that this alteration will not have any significant effect on splicing. Based on the available evidence, this alteration is classified as pathogenic. - |
ARID1B-related BAFopathy Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jun 10, 2021 | - - |
Constipation;C0036572:Seizure;C0349588:Short stature;C2315100:Failure to thrive;C3806482:Recurrent respiratory infections;C4551563:Microcephaly;C5574742:Decreased body weight Uncertain:1
Uncertain significance, flagged submission | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Dec 29, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at