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NM_000092.5(COL4A4):c.2842G>T (p.Gly948Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 18, 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:
RCV001386888.7

Allele description [Variation Report for NM_000092.5(COL4A4):c.2842G>T (p.Gly948Ter)]

NM_000092.5(COL4A4):c.2842G>T (p.Gly948Ter)

Gene:
COL4A4:collagen type IV alpha 4 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q36.3
Genomic location:
Preferred name:
NM_000092.5(COL4A4):c.2842G>T (p.Gly948Ter)
HGVS:
  • NC_000002.12:g.227054612C>A
  • NG_011592.1:g.114948G>T
  • NM_000092.4:c.2842G>T
  • NM_000092.5:c.2842G>TMANE SELECT
  • NP_000083.3:p.Gly948Ter
  • LRG_231t1:c.2842G>T
  • LRG_231:g.114948G>T
  • NC_000002.11:g.227919328C>A
Protein change:
G948*
Links:
dbSNP: rs2150219679
NCBI 1000 Genomes Browser:
rs2150219679
Molecular consequence:
  • NM_000092.5:c.2842G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001587286Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 18, 2020) 		germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Rapid identification of a disease allele in mouse through whole genome sequencing and bulk segregation analysis.

Arnold CN, Xia Y, Lin P, Ross C, Schwander M, Smart NG, Müller U, Beutler B.

Genetics. 2011 Mar;187(3):633-41. doi: 10.1534/genetics.110.124586. Epub 2010 Dec 31.

PubMed [citation]
PMID:
21196518
PMCID:
PMC3063661

Improving mutation screening in familial hematuric nephropathies through next generation sequencing.

Morinière V, Dahan K, Hilbert P, Lison M, Lebbah S, Topa A, Bole-Feysot C, Pruvost S, Nitschke P, Plaisier E, Knebelmann B, Macher MA, Noel LH, Gubler MC, Antignac C, Heidet L.

J Am Soc Nephrol. 2014 Dec;25(12):2740-51. doi: 10.1681/ASN.2013080912. Epub 2014 May 22.

PubMed [citation]
PMID:
24854265
PMCID:
PMC4243343
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001587286.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in COL4A4 are known to be pathogenic (PMID: 21196518, 24854265, 25307543). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has been observed in individual(s) with clinical features of focal segmental glomerulosclerosis and chronic kidney disease (PMID: 30002862). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gly948*) in the COL4A4 gene. It is expected to result in an absent or disrupted protein product.

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

Last Updated: Nov 3, 2024