NM_033380.3(COL4A5):c.1A>G (p.Met1Val) AND X-linked Alport syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 30, 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:: RCV000021092.4

Allele description [Variation Report for NM_033380.3(COL4A5):c.1A>G (p.Met1Val)]

NM_033380.3(COL4A5):c.1A>G (p.Met1Val)

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.1A>G (p.Met1Val)

HGVS:

NC_000023.11:g.108440126A>G
NG_011977.2:g.5203A>G
NG_012059.2:g.4349T>C
NM_000495.5:c.1A>G
NM_033380.3:c.1A>GMANE SELECT
NP_000486.1:p.Met1Val
NP_203699.1:p.Met1Val
LRG_232t1:c.1A>G
LRG_232t2:c.1A>G
LRG_232:g.5203A>G
LRG_232p1:p.Met1Val
LRG_232p2:p.Met1Val
LRG_233:g.4349T>C
NC_000023.10:g.107683356A>G
NG_011977.1:g.5203A>G
NM_000495.4:c.1A>G

Protein change:

M1V

Links:

dbSNP: rs104886050

NCBI 1000 Genomes Browser:

rs104886050

Molecular consequence:

NM_000495.5:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_033380.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_000495.5:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_033380.3:c.1A>G - 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
SCV001425319	Johns Hopkins Genomics, Johns Hopkins University	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 30, 2020)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 8651296, 9195222, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001425319

Johns Hopkins Genomics, Johns Hopkins University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 30, 2020)

germline

clinical testing

PubMed (3)
[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

X-linked Alport syndrome: an SSCP-based mutation survey over all 51 exons of the COL4A5 gene.

Renieri A, Bruttini M, Galli L, Zanelli P, Neri T, Rossetti S, Turco A, Heiskari N, Zhou J, Gusmano R, Massella L, Banfi G, Scolari F, Sessa A, Rizzoni G, Tryggvason K, Pignatti PF, Savi M, Ballabio A, De Marchi M.

Am J Hum Genet. 1996 Jun;58(6):1192-204.

PubMed [citation]

PMID:: 8651296
PMCID:: PMC1915065

The clinical spectrum of type IV collagen mutations.

Lemmink HH, Schröder CH, Monnens LA, Smeets HJ.

Hum Mutat. 1997;9(6):477-99. Review.

PubMed [citation]

PMID:: 9195222

See all PubMed Citations (3)

Details of each submission

From Johns Hopkins Genomics, Johns Hopkins University, SCV001425319.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This variant is predicted to abolish the native initation codon of COL4A5 and has been previously reported in a patient presenting with presumed X-linked dominant Alport syndrome (end stage-renal disease, family history of similar presentations, no information about hearing). Additionally, this COL4A5 variant is absent from a large population dataset. We consider this variant to be pathogenic.

#	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: Sep 29, 2024

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