NM_033380.3(COL4A5):c.466-1G>C AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 11, 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:: RCV001389714.6

Allele description [Variation Report for NM_033380.3(COL4A5):c.466-1G>C]

NM_033380.3(COL4A5):c.466-1G>C

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.466-1G>C

HGVS:

NC_000023.11:g.108573573G>C
NG_011977.2:g.138650G>C
NM_000495.5:c.466-1G>C
NM_033380.3:c.466-1G>CMANE SELECT
LRG_232t1:c.466-1G>C
LRG_232t2:c.466-1G>C
LRG_232:g.138650G>C
NC_000023.10:g.107816803G>C

Links:

dbSNP: rs2147759174

NCBI 1000 Genomes Browser:

rs2147759174

Molecular consequence:

NM_000495.5:c.466-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_033380.3:c.466-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV001591165	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 11, 2020)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 11462238, 26249550, 16199547, 9195222, 10752524, 14514738, 24854265, 26809805, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001591165

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 11, 2020)

germline

clinical testing

PubMed (9)
[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

Detection of mutations in the COL4A5 gene by SSCP in X-linked Alport syndrome.

Hertz JM, Juncker I, Persson U, Matthijs G, Schmidtke J, Petersen MB, Kjeldsen M, Gregersen N.

Hum Mutat. 2001 Aug;18(2):141-8.

PubMed [citation]

PMID:: 11462238

Phenotypic heterogeneity in females with X-linked Alport syndrome.

Allred SC, Weck KE, Gasim A, Mottl AK.

Clin Nephrol. 2015 Nov;84(5):296-300. doi: 10.5414/CN108561.

PubMed [citation]

PMID:: 26249550
PMCID:: PMC4928029

See all PubMed Citations (9)

Details of each submission

From Invitae, SCV001591165.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

Description

Disruption of this splice site has been observed in individual(s) with Alport syndrome (PMID: 11462238, 26249550). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (ExAC no frequency). This sequence change affects an acceptor splice site in intron 8 of the COL4A5 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. For these reasons, this variant has been classified as Pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in COL4A5 are known to be pathogenic (PMID: 9195222, 10752524, 14514738, 24854265, 26809805).

#	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: Mar 5, 2024

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