NM_033380.3(COL4A5):c.4316-1G>T AND X-linked Alport syndrome

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Feb 1, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001002780.4

Allele description [Variation Report for NM_033380.3(COL4A5):c.4316-1G>T]

NM_033380.3(COL4A5):c.4316-1G>T

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.4316-1G>T

HGVS:

NC_000023.11:g.108687481G>T
NG_011977.2:g.252558G>T
NM_000495.5:c.4298-1G>T
NM_033380.3:c.4316-1G>TMANE SELECT
LRG_232t1:c.4298-1G>T
LRG_232t2:c.4316-1G>T
LRG_232:g.252558G>T
NC_000023.10:g.107930711G>T
NM_000495.4:c.4298-1G>T

Links:

dbSNP: rs281874734

NCBI 1000 Genomes Browser:

rs281874734

Molecular consequence:

NM_000495.5:c.4298-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_033380.3:c.4316-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]

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
SCV001160753	Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 25, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001425054	Molecular Biology Laboratory, Fundació Puigvert - KidneyPanel_2020	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 1, 2020)	paternal	research	PubMed (2) [See all records that cite these PMIDs] 25741868, 33532864

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001160753

Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 25, 2019)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001425054

Molecular Biology Laboratory, Fundació Puigvert - KidneyPanel_2020

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 1, 2020)

paternal

research

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	paternal	yes	not provided	not provided	not provided	not provided	not provided	research
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Clinical utility of genetic testing in early-onset kidney disease: seven genes are the main players.

Domingo-Gallego A, Pybus M, Bullich G, Furlano M, Ejarque-Vila L, Lorente-Grandoso L, Ruiz P, Fraga G, López González M, Piñero-Fernández JA, Rodríguez-Peña L, Llano-Rivas I, Sáez R, Bujons-Tur A, Ariceta G, Guirado L, Torra R, Ars E.

Nephrol Dial Transplant. 2022 Mar 25;37(4):687-696. doi: 10.1093/ndt/gfab019.

PubMed [citation]

PMID:: 33532864

Details of each submission

From Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues, SCV001160753.1

#	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	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Molecular Biology Laboratory, Fundació Puigvert - KidneyPanel_2020, SCV001425054.1

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

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

Last Updated: Jun 23, 2024

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