NM_033380.3(COL4A5):c.2858G>T (p.Gly953Val) AND X-linked Alport syndrome

Germline classification:: Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:: Aug 22, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000021452.14

Allele description [Variation Report for NM_033380.3(COL4A5):c.2858G>T (p.Gly953Val)]

NM_033380.3(COL4A5):c.2858G>T (p.Gly953Val)

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.2858G>T (p.Gly953Val)

HGVS:

NC_000023.11:g.108622766G>T
NG_011977.2:g.187843G>T
NM_000495.5:c.2858G>T
NM_033380.3:c.2858G>TMANE SELECT
NP_000486.1:p.Gly953Val
NP_203699.1:p.Gly953Val
NP_203699.1:p.Gly953Val
LRG_232t1:c.2858G>T
LRG_232t2:c.2858G>T
LRG_232:g.187843G>T
LRG_232p1:p.Gly953Val
LRG_232p2:p.Gly953Val
NC_000023.10:g.107865996G>T
NG_011977.1:g.187843G>T
NM_000495.3:c.2858G>T
NM_000495.4:c.2858G>T
NM_033380.1:c.2858G>T
NM_033380.2:c.2858G>T
P29400:p.Gly953Val

Protein change:

G953V

Links:

UniProtKB: P29400#VAR_011263; dbSNP: rs78972735

NCBI 1000 Genomes Browser:

rs78972735

Molecular consequence:

NM_000495.5:c.2858G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_033380.3:c.2858G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: X-linked Alport syndrome (ATS1)
Synonyms:: NEPHROPATHY AND DEAFNESS, X-LINKED; Alport syndrome 1, X-linked recessive; Alport Syndrome and Thin Basement Membrane Nephropathy
Identifiers:: MONDO: MONDO:0010520; MedGen: C4746986; Orphanet: 63; Orphanet: 88917; OMIM: 301050

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000267267	Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 18, 2016)	germline	reference population	PubMed (2) [See all records that cite these PMIDs] 8940267, 25741868
SCV001141995	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2019)	Benign (Aug 22, 2023)	germline	clinical testing	Citation Link,
SCV001716348	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (May 18, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002083652	Natera, Inc.	no assertion criteria provided	Benign (Jul 16, 2020)	germline	clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
East Asian	germline	unknown	not provided	not provided	not provided	not provided	not provided	reference population

Citations

PubMed

Spectrum of mutations in the COL4A5 collagen gene in X-linked Alport syndrome.

Knebelmann B, Breillat C, Forestier L, Arrondel C, Jacassier D, Giatras I, Drouot L, Deschênes G, Grünfeld JP, Broyer M, Gubler MC, Antignac C.

Am J Hum Genet. 1996 Dec;59(6):1221-32.

PubMed [citation]

PMID:: 8940267
PMCID:: PMC1914854

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 Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center, SCV000267267.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	East Asian	not provided	not provided	not provided	reference population	PubMed (2)

#	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

From Mendelics, SCV001141995.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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

From Genome-Nilou Lab, SCV001716348.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Natera, Inc., SCV002083652.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	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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