NM_033380.3(COL4A5):c.2145A>G (p.Lys715=) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 10, 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:: RCV001367174.15

Allele description [Variation Report for NM_033380.3(COL4A5):c.2145A>G (p.Lys715=)]

NM_033380.3(COL4A5):c.2145A>G (p.Lys715=)

Gene:

COL4A5:collagen type IV alpha 5 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq22.3

Genomic location:

Preferred name:

NM_033380.3(COL4A5):c.2145A>G (p.Lys715=)

HGVS:

NC_000023.11:g.108601988A>G
NG_011977.2:g.167065A>G
NM_000495.5:c.2145A>G
NM_033380.3:c.2145A>GMANE SELECT
NP_000486.1:p.Lys715=
NP_203699.1:p.Lys715=
LRG_232t1:c.2145A>G
LRG_232t2:c.2145A>G
LRG_232:g.167065A>G
LRG_232p1:p.Lys715=
LRG_232p2:p.Lys715=
NC_000023.10:g.107845218A>G
NG_011977.1:g.167065A>G

Links:

dbSNP: rs1569495067

NCBI 1000 Genomes Browser:

rs1569495067

Molecular consequence:

NM_000495.5:c.2145A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_033380.3:c.2145A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001563515	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 10, 2020)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26809805, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001563515

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 10, 2020)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Identification of 47 novel mutations in patients with Alport syndrome and thin basement membrane nephropathy.

Weber S, Strasser K, Rath S, Kittke A, Beicht S, Alberer M, Lange-Sperandio B, Hoyer PF, Benz MR, Ponsel S, Weber LT, Klein HG, Hoefele J.

Pediatr Nephrol. 2016 Jun;31(6):941-55. doi: 10.1007/s00467-015-3302-4. Epub 2016 Jan 25.

PubMed [citation]

PMID:: 26809805

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001563515.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 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 Alport syndrome (PMID: 26809805, Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 587206). This variant is not present in population databases (ExAC no frequency). This sequence change affects codon 715 of the COL4A5 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the COL4A5 protein.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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