Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000352.6(ABCC8):c.3544C>T(p.Arg1182Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000186 in 1,613,866 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 Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1182Q) has been classified as Likely pathogenic.
ABCC8 (HGNC:59): (ATP binding cassette subfamily C member 8) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MRP subfamily which is involved in multi-drug resistance. This protein functions as a modulator of ATP-sensitive potassium channels and insulin release. Mutations in the ABCC8 gene and deficiencies in the encoded protein have been observed in patients with hyperinsulinemic hypoglycemia of infancy, an autosomal recessive disorder of unregulated and high insulin secretion. Mutations have also been associated with non-insulin-dependent diabetes mellitus type II, an autosomal dominant disease of defective insulin secretion. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2020]
Verdict is Pathogenic. Variant got 18 ACMG points.
PM1
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PM1 - Located in a mutational hot spot and/or critical and well-established functional domain (e.g., active site of an enzyme) without benign variation
In a topological_domain Cytoplasmic (size 70) in uniprot entity ABCC8_HUMAN there are 18 pathogenic changes around while only 0 benign (100%) in NM_000352.6
PM2
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PM2 - Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
Very rare variant in population databases, with high coverage;
PM5
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PM5 - Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before
Other missense variant is known to change same aminoacid residue: Variant chr11-17404524-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 35611.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
PP3
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PP3 - Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc.)
MetaRNN computational evidence supports a deleterious effect, 0.975
PP5
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PP5 - Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 11-17404525-G-A is Pathogenic according to our data. Variant chr11-17404525-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 210076.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-17404525-G-A is described in Lovd as [Pathogenic].
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Jan 12, 2024
Variant summary: ABCC8 c.3544C>T (p.Arg1182Trp) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251376 control chromosomes. c.3544C>T, also described as p.R1183W, has been reported in the literature in multiple individuals affected with Neonatal diabetes mellitus, and in at-least three cases, this variant arose de novo (Flanagan_2007, Ngoc_2021). Parents carrying this variant were also reported to be unaffected (Flanagan_2007). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 17446535, 34566892). ClinVar contains an entry for this variant (Variation ID: 210076. Pathogenic/Likely pathogenic). Based on the evidence outlined above, the variant was classified as pathogenic. -
Neonatal diabetes mellitus Pathogenic:1
Likely pathogenic, criteria provided, single submitter
clinical testing
Molecular Genetics, Madras Diabetes Research Foundation
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Type 2 diabetes mellitus Pathogenic:1
Pathogenic, no assertion criteria provided
clinical testing
Department of Endocrinology, Antwerp University Hospital
Nov 15, 2020
This is a variant with a reported allele frequency of 0.000003978 according to GnomAD. This, together with Clinvar reports on pathogenicity and variant effect predictor strengthens the indirect evidence for causality. The present mutation has mostly been associated with neonatal diabetes (Flanagan 2007, Batra 2009, Kong 2010, Bonnefond 2013, Beltrand 2015, Zhang 2015, Hashimoto 2016) and in only 3 papers reporting a MODY12 (Reilly 2019, Novak 2020, Gurtunca 2020). -
Genetic Services Laboratory, University of Chicago
Nov 24, 2014
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not provided Pathogenic:1
Pathogenic, criteria provided, single submitter
clinical testing
Invitae
Aug 16, 2023
This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 1182 of the ABCC8 protein (p.Arg1182Trp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of autosomal dominant neonatal diabetes mellitus (PMID: 17446535, 32893419). In at least one individual the variant was observed to be de novo. This variant is also known as R1183W. ClinVar contains an entry for this variant (Variation ID: 210076). Advanced 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 ABCC8 protein function. This variant disrupts the p.Arg1182 amino acid residue in ABCC8. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 16885549, 17446535, 22749773, 24622368). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -