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NM_024844.5(NUP85):c.1430C>T (p.Ala477Val) AND Nephrotic syndrome, type 17

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jan 10, 2019
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:
RCV000721154.2

Allele description [Variation Report for NM_024844.5(NUP85):c.1430C>T (p.Ala477Val)]

NM_024844.5(NUP85):c.1430C>T (p.Ala477Val)

Genes:
GGA3:golgi associated, gamma adaptin ear containing, ARF binding protein 3 [Gene - OMIM - HGNC]
NUP85:nucleoporin 85 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q25.1
Genomic location:
Preferred name:
NM_024844.5(NUP85):c.1430C>T (p.Ala477Val)
HGVS:
  • NC_000017.11:g.75232884C>T
  • NM_001303276.2:c.1292C>T
  • NM_001330472.2:c.1295C>T
  • NM_024844.5:c.1430C>TMANE SELECT
  • NP_001290205.1:p.Ala431Val
  • NP_001317401.1:p.Ala432Val
  • NP_079120.1:p.Ala477Val
  • NC_000017.10:g.73228979C>T
  • NM_024844.4:c.1430C>T
Protein change:
A431V; ALA477VAL
Links:
OMIM: 170285.0001; dbSNP: rs1568094661
NCBI 1000 Genomes Browser:
rs1568094661
Molecular consequence:
  • NM_001303276.2:c.1292C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330472.2:c.1295C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_024844.5:c.1430C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Nephrotic syndrome, type 17
Identifiers:
MONDO: MONDO:0032580; MedGen: C4748545; OMIM: 618176

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000852067OMIM
no assertion criteria provided
Pathogenic
(Nov 12, 2018) 		germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV000899130SIB Swiss Institute of Bioinformatics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jan 10, 2019) 		unknowncuration

PubMed (2)
[See all records that cite these PMIDs]

Description

ClinGen:CA400988934

SCV000899130

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedcuration
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mutations in multiple components of the nuclear pore complex cause nephrotic syndrome.

Braun DA, Lovric S, Schapiro D, Schneider R, Marquez J, Asif M, Hussain MS, Daga A, Widmeier E, Rao J, Ashraf S, Tan W, Lusk CP, Kolb A, Jobst-Schwan T, Schmidt JM, Hoogstraten CA, Eddy K, Kitzler TM, Shril S, Moawia A, Schrage K, et al.

J Clin Invest. 2018 Oct 1;128(10):4313-4328. doi: 10.1172/JCI98688. Epub 2018 Sep 4.

PubMed [citation]
PMID:
30179222
PMCID:
PMC6159964

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From OMIM, SCV000852067.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In an 8-year-old girl (A5195), born of consanguineous Egyptian parents, with nephrotic syndrome type 17 (NPHS17; 618176), Braun et al. (2018) identified a homozygous c.1430C-T transition (c.1430C-T, NM_024844.4) in exon 15 of the NUP85 gene, resulting in an ala477-to-val (A477V) substitution at a highly conserved residue. The mutation was found by high-throughput targeted exon sequencing. The variant was not found in the gnomAD database. The patient had a deceased sister with a similar phenotype; DNA from the sister and parents was not available for segregation studies. Expression of A477V mRNA into nup85-null Xenopus embryos partially rescued the abnormal kidney morphology, suggesting that this allele may have some residual function.

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

From SIB Swiss Institute of Bioinformatics, SCV000899130.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (2)

Description

This variant is interpreted as a Uncertain significance for Nephrotic syndrome 17, autosomal recessive. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PP3 => Multiple lines of computational evidence support a deleterious effect on the gene or gene product.

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

Last Updated: Apr 23, 2022