ClinVar Genomic variation as it relates to human health
NM_000352.6(ABCC8):c.1858C>T (p.Arg620Cys)
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.
Uncertain significance(1); Benign(2); Likely benign(5)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000352.6(ABCC8):c.1858C>T (p.Arg620Cys)
Variation ID: 210071 Accession: VCV000210071.25
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 11p15.1 11: 17428630 (GRCh38) [ NCBI UCSC ] 11: 17450177 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 Oct 5, 2015 Feb 20, 2024 Jan 31, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000352.6:c.1858C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000343.2:p.Arg620Cys missense NM_001287174.3:c.1858C>T NP_001274103.1:p.Arg620Cys missense NM_001351295.2:c.1858C>T NP_001338224.1:p.Arg620Cys missense NM_001351296.2:c.1855C>T NP_001338225.1:p.Arg619Cys missense NM_001351297.2:c.1855C>T NP_001338226.1:p.Arg619Cys missense NR_147094.2:n.1924C>T non-coding transcript variant NC_000011.10:g.17428630G>A NC_000011.9:g.17450177G>A NG_008867.1:g.53273C>T LRG_790:g.53273C>T LRG_790t1:c.1858C>T LRG_790p1:p.Arg620Cys LRG_790t2:c.1858C>T LRG_790p2:p.Arg620Cys Q09428:p.Arg620Cys - Protein change
- R620C, R619C
- Other names
- -
- Canonical SPDI
- NC_000011.10:17428629:G:A
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
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.
-
0.00200 (A)
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
The Genome Aggregation Database (gnomAD), exomes 0.00069
Exome Aggregation Consortium (ExAC) 0.00082
1000 Genomes Project 0.00200
1000 Genomes Project 30x 0.00219
The Genome Aggregation Database (gnomAD) 0.00272
Trans-Omics for Precision Medicine (TOPMed) 0.00306
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00362
- 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 | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
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. |
|||
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. |
---|---|---|---|---|
Likely benign (2) |
criteria provided, multiple submitters, no conflicts
|
Sep 29, 2022 | RCV000193433.7 | |
Conflicting interpretations of pathogenicity (2) |
criteria provided, conflicting classifications
|
Aug 22, 2023 | RCV000671926.6 | |
Likely benign (6) |
criteria provided, multiple submitters, no conflicts
|
Jan 31, 2024 | RCV000952127.14 | |
Benign (1) |
criteria provided, single submitter
|
Dec 7, 2018 | RCV001174394.3 | |
Hereditary hyperinsulinism
|
Benign (1) |
no assertion criteria provided
|
Dec 24, 2019 | RCV001274301.2 |
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. |
|
---|---|---|---|---|---|
Likely benign
(Mar 19, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Genetic Services Laboratory, University of Chicago
Accession: SCV000246291.1
First in ClinVar: Oct 05, 2015 Last updated: Oct 05, 2015 |
|
|
Uncertain significance
(Jan 05, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Hyperinsulinemic hypoglycemia, familial, 1
Affected status: unknown
Allele origin:
unknown
|
Counsyl
Accession: SCV000796962.1
First in ClinVar: Aug 05, 2018 Last updated: Aug 05, 2018 |
|
|
Benign
(Dec 07, 2018)
|
criteria provided, single submitter
Method: research
|
Monogenic diabetes
Affected status: unknown
Allele origin:
unknown
|
Personalized Diabetes Medicine Program, University of Maryland School of Medicine
Accession: SCV001337532.1
First in ClinVar: Jun 14, 2020 Last updated: Jun 14, 2020 |
Comment:
ACMG criteria: BS2 (23 cases and 24 controls in type2diabetesgenetics.org) + BS1 (0.9% MAF in gnomAD African pop) = benign (REVEL 0.445 + PP3/8 predictors … (more)
ACMG criteria: BS2 (23 cases and 24 controls in type2diabetesgenetics.org) + BS1 (0.9% MAF in gnomAD African pop) = benign (REVEL 0.445 + PP3/8 predictors + BP4/2 predictors = conflicting evidence, not using). Variant found in 46-year old male with T2DM, not overweight, treated with SU (PMID: 22210575); Reported to cause HI of infancy (AR) in summary table in PMID 23226049 (less)
Number of individuals with the variant: 1
|
|
Likely benign
(May 03, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV001757904.1
First in ClinVar: Jul 24, 2021 Last updated: Jul 24, 2021 |
Comment:
This variant is associated with the following publications: (PMID: 31604004, 23275527, 28095440, 22995991, 22210575, 20849526, 10204114, 20981092, 23771920)
|
|
Likely benign
(Sep 29, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV002598613.1
First in ClinVar: Nov 05, 2022 Last updated: Nov 05, 2022 |
Comment:
Variant summary: ABCC8 c.1858C>T (p.Arg620Cys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging … (more)
Variant summary: ABCC8 c.1858C>T (p.Arg620Cys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00069 in 251124 control chromosomes, predominantly at a frequency of 0.0094 within the African or African-American subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 2.8 fold of the estimated maximal expected allele frequency for a pathogenic variant in ABCC8 causing Familial Hyperinsulinism phenotype (0.0034), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. c.1858C>T has been reported in the literature as a non-informative genotype (unclear inheritance pattern) in settings of Familial Hyperinsulinism, Adult onset Type 2 diabetes and Gestational Diabetes (example, Lang_2010, Riveleine_2012, Doddabelavangala Mruthyunjaya_2017). These report(s) do not provide unequivocal conclusions about association of the variant with Familial Hyperinsulinism. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with a predominant consensus as benign/likely benign (n=5) (VUS, n=2). Based on the evidence outlined above, the variant was classified as likely benign. (less)
|
|
Benign
(Aug 22, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Hyperinsulinemic hypoglycemia, familial, 1
Affected status: unknown
Allele origin:
germline
|
Mendelics
Accession: SCV001138234.2
First in ClinVar: Jan 09, 2020 Last updated: Aug 25, 2023 |
|
|
Likely benign
(Jan 31, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001098602.6
First in ClinVar: Dec 17, 2019 Last updated: Feb 20, 2024 |
|
|
Likely benign
(Nov 22, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV004562089.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
|
|
Benign
(Dec 24, 2019)
|
no assertion criteria provided
Method: clinical testing
|
Hereditary hyperinsulinism
Affected status: unknown
Allele origin:
germline
|
Natera, Inc.
Accession: SCV001458273.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
|
|
Uncertain significance
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
unknown
|
Department of Pathology and Laboratory Medicine, Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001551133.1 First in ClinVar: Apr 13, 2021 Last updated: Apr 13, 2021 |
Comment:
The ABCC8 p.Arg620Cys variant was identified in 2 of 378 proband chromosomes (frequency: 0.0053) from individuals or families with Maturity Onset Diabetes of the Young … (more)
The ABCC8 p.Arg620Cys variant was identified in 2 of 378 proband chromosomes (frequency: 0.0053) from individuals or families with Maturity Onset Diabetes of the Young (MODY) or Type 2 diabetes (Doddabelavangala_2017_PMID:28095440; Riveline_2012_PMID:22210575). The variant was also identified in dbSNP (ID: rs58241708), ClinVar (classified as likely benign by Genetic Services Laboratory, University of Chicago and as a VUS by Counsyl) and LOVD 3.0. The variant was identified in control databases in 253 of 282492 chromosomes (1 homozygous) at a frequency of 0.000896 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 231 of 24964 chromosomes (freq: 0.009253), Latino in 10 of 35424 chromosomes (freq: 0.000282), Other in 2 of 7222 chromosomes (freq: 0.000277), Ashkenazi Jewish in 2 of 10360 chromosomes (freq: 0.000193), South Asian in 5 of 30616 chromosomes (freq: 0.000163) and European (non-Finnish) in 3 of 129052 chromosomes (freq: 0.000023), while the variant was not observed in the East Asian or European (Finnish) populations. The p.Arg620 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. (less)
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV002035046.1 First in ClinVar: Dec 18, 2021 Last updated: Dec 18, 2021 |
|
|
Likely benign
(-)
|
no assertion criteria provided
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV002037089.1 First in ClinVar: Dec 18, 2021 Last updated: Dec 18, 2021 |
|
|
click to load more click to collapse |
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 |
---|---|---|---|---|
Comprehensive Maturity Onset Diabetes of the Young (MODY) Gene Screening in Pregnant Women with Diabetes in India. | Doddabelavangala Mruthyunjaya M | PloS one | 2017 | PMID: 28095440 |
Large-scale pooled next-generation sequencing of 1077 genes to identify genetic causes of short stature. | Wang SR | The Journal of clinical endocrinology and metabolism | 2013 | PMID: 23771920 |
Genotype and phenotype correlations in 417 children with congenital hyperinsulinism. | Snider KE | The Journal of clinical endocrinology and metabolism | 2013 | PMID: 23275527 |
Clinical and metabolic features of adult-onset diabetes caused by ABCC8 mutations. | Riveline JP | Diabetes care | 2012 | PMID: 22210575 |
The molecular mechanisms and pharmacotherapy of ATP-sensitive potassium channel gene mutations underlying neonatal diabetes. | Lang V | Pharmacogenomics and personalized medicine | 2010 | PMID: 23226049 |
Diagnosis and localization of focal congenital hyperinsulinism by 18F-fluorodopa PET scan. | Hardy OT | The Journal of pediatrics | 2007 | PMID: 17236890 |
Mutations in the genes encoding the pancreatic beta-cell KATP channel subunits Kir6.2 (KCNJ11) and SUR1 (ABCC8) in diabetes mellitus and hyperinsulinism. | Gloyn AL | Human mutation | 2006 | PMID: 16416420 |
Persistent hyperinsulinaemic hyperglycaemia of infancy-derived cells; implications for beta-cells that replicate in vitro. | Dunne MJ | Journal of molecular endocrinology | 2000 | PMID: 10828824 |
Familial hyperinsulinism and pancreatic beta-cell ATP-sensitive potassium channels. | Sharma N | Kidney international | 2000 | PMID: 10720932 |
Hyperinsulinism of infancy: towards an understanding of unregulated insulin release. European Network for Research into Hyperinsulinism in Infancy. | Shepherd RM | Archives of disease in childhood. Fetal and neonatal edition | 2000 | PMID: 10685980 |
Genetics of neonatal hyperinsulinism. | Glaser B | Archives of disease in childhood. Fetal and neonatal edition | 2000 | PMID: 10685979 |
Molecular biology of adenosine triphosphate-sensitive potassium channels. | Aguilar-Bryan L | Endocrine reviews | 1999 | PMID: 10204114 |
type2diabetesgenetics.org | - | - | - | - |
click to load more click to collapse |
Text-mined citations for rs58241708 ...
HelpRecord last updated Sep 29, 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.