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NM_003661.3(APOL1):c.[1024A>G;1152T>G] AND Hyalinosis, Segmental Glomerular

Germline classification:
risk factor (1 submission)
Last evaluated:
Mar 4, 2020
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001195215.5

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]
Observations:
29

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]
Observations:
29

Condition(s)

Name:
Hyalinosis, Segmental Glomerular
Identifiers:
MeSH: D005923; MedGen: C0086432

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001365522Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
risk factor
(Mar 4, 2020)
germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown2929not providednot providednot providedclinical testing

Citations

PubMed

A tripartite complex of suPAR, APOL1 risk variants and α(v)β(3) integrin on podocytes mediates chronic kidney disease.

Hayek SS, Koh KH, Grams ME, Wei C, Ko YA, Li J, Samelko B, Lee H, Dande RR, Lee HW, Hahm E, Peev V, Tracy M, Tardi NJ, Gupta V, Altintas MM, Garborcauskas G, Stojanovic N, Winkler CA, Lipkowitz MS, Tin A, Inker LA, et al.

Nat Med. 2017 Aug;23(8):945-953. doi: 10.1038/nm.4362. Epub 2017 Jun 26.

PubMed [citation]
PMID:
28650456
PMCID:
PMC6019326

Sequencing rare and common APOL1 coding variants to determine kidney disease risk.

Limou S, Nelson GW, Lecordier L, An P, O'hUigin CS, David VA, Binns-Roemer EA, Guiblet WM, Oleksyk TK, Pays E, Kopp JB, Winkler CA.

Kidney Int. 2015 Oct;88(4):754-63. doi: 10.1038/ki.2015.151. Epub 2015 May 20.

PubMed [citation]
PMID:
25993319
PMCID:
PMC4591109
See all PubMed Citations (7)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV001365522.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided29not providednot providedclinical testing PubMed (7)

Description

APOL1 c.[1024A>G;1152T>G] (p.[Ser342Gly;Ile384Met]), traditionally referred to as G1, 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 between 9.66-47.4 for developing FSGS/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, OR=9.66 [95% CI not given, P<0.00001] Limou 2015). In vitro and in vivo studies provide evidence that these alleles impact protein function (Beckerman 2017, Hayek 2017). In summary, this variant is an established risk factor for chronic kidney disease in homozygous state.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided29not provided29not provided

Last Updated: Jul 23, 2024