ClinVar Genomic variation as it relates to human health
NM_000352.6(ABCC8):c.4477C>T (p.Arg1493Trp)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Pathogenic(5); Likely pathogenic(1); Uncertain risk allele(2)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000352.6(ABCC8):c.4477C>T (p.Arg1493Trp)
Variation ID: 9096 Accession: VCV000009096.15
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11p15.1 11: 17394334 (GRCh38) [ NCBI UCSC ] 11: 17415881 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Apr 4, 2013 Jun 17, 2024 May 11, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000352.6:c.4477C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000343.2:p.Arg1493Trp missense NM_001287174.3:c.4480C>T NP_001274103.1:p.Arg1494Trp missense NM_001351295.2:c.4543C>T NP_001338224.1:p.Arg1515Trp missense NM_001351296.2:c.4477C>T NP_001338225.1:p.Arg1493Trp missense NM_001351297.2:c.4474C>T NP_001338226.1:p.Arg1492Trp missense NR_147094.2:n.4772C>T non-coding transcript variant NC_000011.10:g.17394334G>A NC_000011.9:g.17415881G>A NG_008867.1:g.87569C>T LRG_790:g.87569C>T LRG_790t1:c.4477C>T LRG_790p1:p.Arg1493Trp LRG_790t2:c.4480C>T LRG_790p2:p.Arg1494Trp Q09428:p.Arg1493Trp - Protein change
- R1494W, R1493W, R1515W, R1492W
- Other names
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NM_000352.6(ABCC8):c.4477C>T
- Canonical SPDI
- NC_000011.10:17394333:G:A
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00002
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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ABCC8 | - | - |
GRCh38 GRCh37 |
2370 | 2502 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Conflicting interpretations of pathogenicity (5) |
criteria provided, conflicting classifications
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May 11, 2024 | RCV000009664.13 | |
Hereditary hyperinsulinism
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Pathogenic (1) |
no assertion criteria provided
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May 2, 2021 | RCV001831558.3 |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Dec 4, 2023 | RCV000710390.11 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 8, 2023 | RCV003466844.1 | |
Uncertain risk allele (1) |
criteria provided, single submitter
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May 11, 2024 | RCV004549354.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely pathogenic
(Mar 24, 2014)
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criteria provided, single submitter
Method: literature only
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Persistent hyperinsulinemic hypoglycemia of infancy
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
unknown
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Counsyl
Accession: SCV000220188.2
First in ClinVar: Mar 29, 2015 Last updated: Dec 24, 2022 |
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Pathogenic
(Aug 16, 2023)
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criteria provided, single submitter
Method: curation
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Hyperinsulinemic hypoglycemia, familial, 1
(Autosomal recessive inheritance)
Affected status: unknown
Allele origin:
germline
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Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard
Accession: SCV004026546.1
First in ClinVar: Aug 19, 2023 Last updated: Aug 19, 2023 |
Comment:
The p.Arg1493Trp variant in ABCC8 has been reported in at least 9 individuals with hyperinsulinemic hypoglycemia (PMID: 30186238, 33688939, 10202168, 10426386, 19475716, 9769320, 15579781), segregated … (more)
The p.Arg1493Trp variant in ABCC8 has been reported in at least 9 individuals with hyperinsulinemic hypoglycemia (PMID: 30186238, 33688939, 10202168, 10426386, 19475716, 9769320, 15579781), segregated with disease in 2 affected relatives from 2 families (PMID: 19475716), and has been identified in 0.003% (1/30616) of South Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs28936371). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (Variation ID#: 9096) and has been interpreted as pathogenic or likely pathogenic by multiple sources. Of the 9 affected individuals, at least 4 were compound heterozygotes that carried a reported pathogenic variants in trans, which increases the likelihood that the p.Arg1493Trp variant is pathogenic (PMID: 30186238, 9769320). In vitro functional studies provide some evidence that the p.Arg1493Trp variant may slightly impact protein function (PMID: 15579781). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive hyperinsulinemic hypoglycemia. ACMG/AMP Criteria applied: PM3_very-strong, PP3, PP2_supporting, PS3_supporting, PP1 (Richards 2015). (less)
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Pathogenic
(Sep 08, 2023)
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criteria provided, single submitter
Method: clinical testing
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Type 2 diabetes mellitus
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004194318.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Dec 04, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001221921.5
First in ClinVar: Apr 15, 2020 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 1493 of the ABCC8 protein … (more)
This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 1493 of the ABCC8 protein (p.Arg1493Trp). This variant is present in population databases (rs28936371, gnomAD 0.003%). This missense change has been observed in individuals with autosomal recessive diffuse or focal hyperinsulinism (PMID: 9769320, 15579781, 30186238). This variant is also known as R1494W. ClinVar contains an entry for this variant (Variation ID: 9096). 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 with a positive predictive value of 95%. Experimental studies have shown that this missense change affects ABCC8 function (PMID: 15579781). This variant disrupts the p.Arg1493 amino acid residue in ABCC8. Other variant(s) that disrupt this residue have been observed in individuals with ABCC8-related conditions (PMID: 10426386), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. (less)
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Uncertain risk allele
(May 11, 2024)
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criteria provided, single submitter
(K & H Uppaluri Personalized Medicine Clinic Variant Classification & Assertion Criteria_Updated V.1)
Method: research
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Hyperinsulinemic hypoglycemia, familial, 1
(Somatic mutation)
Affected status: unknown
Allele origin:
somatic
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Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic
Accession: SCV002513288.2
First in ClinVar: May 21, 2022 Last updated: May 19, 2024 |
Comment:
This variant is found to be a potent moderate impact, deleterious variant with a CADD score of 29.3 and sufficient scientific evidence to support gene-disease … (more)
This variant is found to be a potent moderate impact, deleterious variant with a CADD score of 29.3 and sufficient scientific evidence to support gene-disease correlation. This is found more frequently in congenital Hyperinsulinism cases as per recent evidence as well. However, since this is not a high impact variant and has limited evidence, this variant is reclassified as Uncertain risk allele only. (less)
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Uncertain risk allele
(May 11, 2024)
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criteria provided, single submitter
(K & H Uppaluri Personalized Medicine Clinic Variant Classification & Assertion Criteria_Updated V.1)
Method: research
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Diabetes mellitus, transient neonatal, 2
(Somatic mutation)
Affected status: unknown
Allele origin:
somatic
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Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic
Accession: SCV002513289.2
First in ClinVar: May 21, 2022 Last updated: May 19, 2024 |
Comment:
This variant is found to be a potent moderate impact, deleterious variant with a CADD score of 29.3 and sufficient scientific evidence of gene-disease correlation. … (more)
This variant is found to be a potent moderate impact, deleterious variant with a CADD score of 29.3 and sufficient scientific evidence of gene-disease correlation. However, since this is not a high impact variant and no variant evidence, this variant is reclassified as Uncertain risk allele. (less)
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Pathogenic
(Feb 01, 2024)
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criteria provided, single submitter
Method: curation
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Hyperinsulinemic hypoglycemia, familial, 1
Affected status: no
Allele origin:
germline
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Laboratory of Medical Genetics, National & Kapodistrian University of Athens
Accession: SCV005051721.1
First in ClinVar: Jun 17, 2024 Last updated: Jun 17, 2024 |
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Pathogenic
(Aug 29, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Athena Diagnostics
Accession: SCV000840600.1
First in ClinVar: Oct 20, 2018 Last updated: Oct 20, 2018 |
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Pathogenic
(Oct 01, 1998)
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no assertion criteria provided
Method: literature only
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HYPERINSULINEMIC HYPOGLYCEMIA, FAMILIAL, 1
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000029882.2
First in ClinVar: Apr 04, 2013 Last updated: May 04, 2020 |
Comment on evidence:
In 2 unrelated sporadic cases of persistent hyperinsulinemic hypoglycemia of infancy (HHF1; 256450) due to focal adenomatous hyperplasia, Verkarre et al. (1998) demonstrated loss of … (more)
In 2 unrelated sporadic cases of persistent hyperinsulinemic hypoglycemia of infancy (HHF1; 256450) due to focal adenomatous hyperplasia, Verkarre et al. (1998) demonstrated loss of heterozygosity of the 11p15 region in the maternal allele and a point mutation in the paternally derived SUR allele: a 4480C-T transition in exon 37 leading to an arg1494-to-trp (R1494W) substitution. The father in each case was heterozygous for the R1494W mutation. (less)
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Pathogenic
(May 02, 2021)
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no assertion criteria provided
Method: clinical testing
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Hereditary hyperinsulinism
Affected status: unknown
Allele origin:
germline
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Natera, Inc.
Accession: SCV002085270.1
First in ClinVar: Feb 13, 2022 Last updated: Feb 13, 2022 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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ABCC8-Related Maturity-Onset Diabetes of the Young (MODY12): A Report of a Chinese Family. | Lin L | Frontiers in endocrinology | 2020 | PMID: 33013711 |
New insights into K(ATP) channel gene mutations and neonatal diabetes mellitus. | Pipatpolkai T | Nature reviews. Endocrinology | 2020 | PMID: 32376986 |
Intraoperative Ultrasound: A Tool to Support Tissue-Sparing Curative Pancreatic Resection in Focal Congenital Hyperinsulinism. | Bendix J | Frontiers in endocrinology | 2018 | PMID: 30186238 |
Transient neonatal diabetes mellitus caused by a de novoABCC8 gene mutation. | Kong JH | Korean journal of pediatrics | 2011 | PMID: 21738553 |
Familial focal congenital hyperinsulinism. | Ismail D | The Journal of clinical endocrinology and metabolism | 2011 | PMID: 20943779 |
Permanent neonatal diabetes due to activating mutations in ABCC8 and KCNJ11. | Edghill EL | Reviews in endocrine & metabolic disorders | 2010 | PMID: 20922570 |
The spectrum of ABCC8 mutations in Norwegian patients with congenital hyperinsulinism of infancy. | Sandal T | Clinical genetics | 2009 | PMID: 19475716 |
Update of mutations in the genes encoding the pancreatic beta-cell K(ATP) channel subunits Kir6.2 (KCNJ11) and sulfonylurea receptor 1 (ABCC8) in diabetes mellitus and hyperinsulinism. | Flanagan SE | Human mutation | 2009 | PMID: 18767144 |
Mutations in the ABCC8 gene encoding the SUR1 subunit of the KATP channel cause transient neonatal diabetes, permanent neonatal diabetes or permanent diabetes diagnosed outside the neonatal period. | Patch AM | Diabetes, obesity & metabolism | 2007 | PMID: 17919176 |
New ABCC8 mutations in relapsing neonatal diabetes and clinical features. | Vaxillaire M | Diabetes | 2007 | PMID: 17389331 |
Genotype-phenotype associations in patients with severe hyperinsulinism of infancy. | Greer RM | Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society | 2007 | PMID: 17378627 |
Hyperinsulinism of infancy: novel ABCC8 and KCNJ11 mutations and evidence for additional locus heterogeneity. | Tornovsky S | The Journal of clinical endocrinology and metabolism | 2004 | PMID: 15579781 |
Unbalanced expression of 11p15 imprinted genes in focal forms of congenital hyperinsulinism: association with a reduction to homozygosity of a mutation in ABCC8 or KCNJ11. | Fournet JC | The American journal of pathology | 2001 | PMID: 11395395 |
Hyperinsulinism caused by paternal-specific inheritance of a recessive mutation in the sulfonylurea-receptor gene. | Glaser B | Diabetes | 1999 | PMID: 10426386 |
Clinical features of 52 neonates with hyperinsulinism. | de Lonlay-Debeney P | The New England journal of medicine | 1999 | PMID: 10202168 |
Paternal mutation of the sulfonylurea receptor (SUR1) gene and maternal loss of 11p15 imprinted genes lead to persistent hyperinsulinism in focal adenomatous hyperplasia. | Verkarre V | The Journal of clinical investigation | 1998 | PMID: 9769320 |
Spectrophotometric determination of quinine, emethine and ephedrine in pharmaceutical preparations with tetrabromophenolphthalein ethyl ester by solvent extraction. | Sakai T | Chemical & pharmaceutical bulletin | 1976 | PMID: 1021286 |
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Text-mined citations for rs28936371 ...
HelpRecord last updated Nov 10, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.