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NM_003661.3(APOL1):c.[1024A>G;1152T>G] AND Focal segmental glomerulosclerosis, susceptibility to

Germline classification:
Established risk allele (1 submission)
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV002468554.3

Alleles description [Variation Report for NM_003661.3(APOL1):c.[1024A>G;1152T>G]]

NM_003661.4(APOL1):c.1024A>G (p.Ser342Gly)

Gene:
APOL1:apolipoprotein L1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q12.3
Genomic location:
Preferred name:
NM_003661.4(APOL1):c.1024A>G (p.Ser342Gly)
HGVS:
  • NC_000022.11:g.36265860A>G
  • NG_023228.1:g.17790A>G
  • NM_001136540.2:c.1024A>G
  • NM_001136541.2:c.970A>G
  • NM_001362927.2:c.970A>G
  • NM_003661.4:c.1024A>GMANE SELECT
  • NM_145343.3:c.1072A>G
  • NP_001130012.1:p.Ser342Gly
  • NP_001130013.1:p.Ser324Gly
  • NP_001349856.1:p.Ser324Gly
  • NP_003652.2:p.Ser342Gly
  • NP_663318.1:p.Ser358Gly
  • NP_663318.1:p.Ser358Gly
  • LRG_169t1:c.1072A>G
  • LRG_169:g.17790A>G
  • LRG_169p1:p.Ser358Gly
  • NC_000022.10:g.36661906A>G
  • NM_003661.3:c.1024A>G
  • NM_145343.2:c.1072A>G
  • c.1024A>G (p.Ser342Gly)
Protein change:
S324G; Ser358Gly
Links:
OMIM: 603743.0001; dbSNP: rs73885319
NCBI 1000 Genomes Browser:
rs73885319
Molecular consequence:
  • NM_001136540.2:c.1024A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136541.2:c.970A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001362927.2:c.970A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003661.4:c.1024A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_145343.3:c.1072A>G - missense variant - [Sequence Ontology: SO:0001583]

NM_003661.4(APOL1):c.1152T>G (p.Ile384Met)

Gene:
APOL1:apolipoprotein L1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q12.3
Genomic location:
Preferred name:
NM_003661.4(APOL1):c.1152T>G (p.Ile384Met)
HGVS:
  • NC_000022.11:g.36265988T>G
  • NG_023228.1:g.17918T>G
  • NM_001136540.2:c.1152T>G
  • NM_001136541.2:c.1098T>G
  • NM_001362927.2:c.1098T>G
  • NM_003661.4:c.1152T>GMANE SELECT
  • NM_145343.3:c.1200T>G
  • NP_001130012.1:p.Ile384Met
  • NP_001130013.1:p.Ile366Met
  • NP_001349856.1:p.Ile366Met
  • NP_003652.2:p.Ile384Met
  • NP_663318.1:p.Ile400Met
  • NP_663318.1:p.Ile400Met
  • LRG_169t1:c.1200T>G
  • LRG_169:g.17918T>G
  • LRG_169p1:p.Ile400Met
  • NC_000022.10:g.36662034T>G
  • NM_003661.3:c.1152T>G
  • NM_145343.2:c.1200T>G
Protein change:
I366M
Links:
OMIM: 603743.0001; dbSNP: rs60910145
NCBI 1000 Genomes Browser:
rs60910145
Molecular consequence:
  • NM_001136540.2:c.1152T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001136541.2:c.1098T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001362927.2:c.1098T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003661.4:c.1152T>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_145343.3:c.1200T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Focal segmental glomerulosclerosis, susceptibility to
Identifiers:

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002764632Department of Pathology and Laboratory Medicine, Sinai Health System
no assertion criteria provided
Established risk alleleunknownresearch

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedresearch

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System, SCV002764632.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedresearchnot provided

Description

The APOL1 c.[1024A>G;1152T>G]; p.[Ser342Gly;Ile384Met] (ALIAS: c.[1072A>G; 1200T>G]; p.[Ser358Gly; Ile400Met]) variant, otherwise known as the G1 allele/haplotype, has been associated with increased risk for multiple renal diseases in African Americans, particularly focal segmental glomerulosclerosis (FSGS), as well as an increased risk for end-stage kidney disease (ESKD). This variant is common in individuals of African ancestry (23%, Genome Aggregation Database (gnomAD); rs73885319 and rs60910145) and is present in ClinVar (ID: 6080). Several small case-control studies have reported odds ratios (ORs) between 9.66-47.4 for developing FSGS/HIV-associated nephropathy (HIVAN) in homozygous individuals (OR=47.4 [95% CI 11.9-231.5] for HIVAN and OR=23.2 [95% CI 12-46.7] for FSGS (Kopp_2011_21997394), OR=9.66 [95% CI not given, P<0.00001] (Limou_2015_25993319)). In a recessive model, individuals carrying any combination of two APOL1 risk alleles had 89-fold higher odds (95% confidence interval, 18 to 912; P<0.001) of developing HIV-associated nephropathy compared with HIV-positive controls (Kasembeli_2015_25788523). More evidence is available in the literature demonstrating an increased odds ratio of various (but not all) kidney and glomerular diseases in persons carrying two of the risk alleles, i.e. G1/G1, G2/G2 and compound heterozygous G1/G2 (PMID: 25100047, 25788523, 21997394, 23766536, 24504811, 23520206, 24731740, 32561682, 33576823, 34352311, 34670811). Mechanistically, the G1 and G2 variants appear to act as gain-of-function, increasing APOL1 channel activity (PMID: 33380423, 32427098) and APOL1-mediated cytotoxicity (PMID: 26091559, 26699492, 32427098, 24899058, 26089538). In vitro and in vivo studies provide evidence that these alleles impact protein function (Beckerman 2017, Hayek 2017). In summary, the presence of two copies of the APOL1 risk variants G1 and/or G2 (ClinVar Variation IDs: 6080 and 6081) is definitively associated with an increased susceptibility to multiple glomerular and hypertensive kidney diseases, most prominently FSGS and HIVAN (OMIM:612551). The preferred disease name suggested for this grouping of disorders is ‘Glomerulopathy, susceptibility - APOL1’. (Adapted from: Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine; Accession: SCV001365522.1 AND ClinGen: APOL1 - focal segmental glomerulosclerosis 4, susceptibility to). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant meets our laboratory's criteria to be classified as a likely pathogenic - risk factor in association with susceptibility to focal segmental glomerulosclerosis when present in the homozygous or compound heterozygous (with G2 allele) state.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 15, 2024