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NM_000213.5(ITGB4):c.2929C>T (p.Arg977Cys) AND Nephrotic syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 24, 2018
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:
RCV001328148.2

Allele description [Variation Report for NM_000213.5(ITGB4):c.2929C>T (p.Arg977Cys)]

NM_000213.5(ITGB4):c.2929C>T (p.Arg977Cys)

Gene:
ITGB4:integrin subunit beta 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q25.1
Genomic location:
Preferred name:
NM_000213.5(ITGB4):c.2929C>T (p.Arg977Cys)
HGVS:
  • NC_000017.11:g.75742728C>T
  • NG_007372.1:g.26294C>T
  • NM_000213.5:c.2929C>TMANE SELECT
  • NM_001005619.1:c.2929C>T
  • NM_001005731.3:c.2929C>T
  • NM_001321123.2:c.2929C>T
  • NP_000204.3:p.Arg977Cys
  • NP_001005619.1:p.Arg977Cys
  • NP_001005731.1:p.Arg977Cys
  • NP_001308052.1:p.Arg977Cys
  • NC_000017.10:g.73738809C>T
  • NM_000213.3:c.2929C>T
  • NM_000213.4:c.2929C>T
  • NM_001005731.1:c.2929C>T
  • NM_001005731.2:c.2929C>T
Protein change:
R977C
Links:
dbSNP: rs145976111
NCBI 1000 Genomes Browser:
rs145976111
Molecular consequence:
  • NM_000213.5:c.2929C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005619.1:c.2929C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001005731.3:c.2929C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321123.2:c.2929C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Nephrotic syndrome
Identifiers:
MONDO: MONDO:0005377; MedGen: C0027726; Human Phenotype Ontology: HP:0000100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001449345Sydney Genome Diagnostics, Children's Hospital Westmead
no assertion criteria provided
Uncertain significance
(Oct 24, 2018) 		unknownclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownyes1not providednot providednot providednot providedclinical testing

Details of each submission

From Sydney Genome Diagnostics, Children's Hospital Westmead, SCV001449345.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

This patient is heterozygous for a variant of unknown clinical significance (VOUS), c.2929C>T (p.Arg977Cys), in the ITGB4 gene. To our knowledge, this variant has not been previously reported in the literature to be associated with disease. It has been listed in Exome Aggregation Consortium (ExAC) with a frequency of 335 out of 117600 alleles (0.2%). p.Arg977, is a highly conserved amino acid (up to 11 species) and there is also a large physicochemical difference between the wild type arginine and mutant cysteine. In silico analysis (Alamut Visual v2.6) using Align GVGD, PolyPhen2, SIFT and Mutation Taster all suggest that this variant is likely to be pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided1not providednot providednot provided

Last Updated: May 12, 2024