NM_033380.3(COL4A5):c.3403A>G (p.Ile1135Val) AND X-linked Alport syndrome

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Dec 11, 2020
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:: RCV001089923.11

Allele description [Variation Report for NM_033380.3(COL4A5):c.3403A>G (p.Ile1135Val)]

NM_033380.3(COL4A5):c.3403A>G (p.Ile1135Val)

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.3403A>G (p.Ile1135Val)

HGVS:

NC_000023.11:g.108665536A>G
NG_011977.2:g.230613A>G
NM_000495.5:c.3403A>G
NM_033380.3:c.3403A>GMANE SELECT
NP_000486.1:p.Ile1135Val
NP_203699.1:p.Ile1135Val
LRG_232t1:c.3403A>G
LRG_232t2:c.3403A>G
LRG_232:g.230613A>G
LRG_232p1:p.Ile1135Val
LRG_232p2:p.Ile1135Val
NC_000023.10:g.107908766A>G
NG_011977.1:g.230613A>G
NM_000495.4:c.3403A>G
NM_033380.1:c.3403A>G
NM_033380.2:c.3403A>G

Protein change:

I1135V

Links:

dbSNP: rs747614562

NCBI 1000 Genomes Browser:

rs747614562

Molecular consequence:

NM_000495.5:c.3403A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_033380.3:c.3403A>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

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001245124	Medical Genetics, University of Parma	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 11, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001465822	Natera, Inc.	no assertion criteria provided	Likely benign (Sep 9, 2020)	germline	clinical testing
SCV002047708	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2021)	Likely benign (Dec 11, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001245124

Medical Genetics, University of Parma

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 11, 2020)

germline

clinical testing

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

SCV001465822

Natera, Inc.

no assertion criteria provided

Likely benign
(Sep 9, 2020)

germline

clinical testing

SCV002047708

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)

Likely benign
(Dec 11, 2020)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	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

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

Details of each submission

From Medical Genetics, University of Parma, SCV001245124.1

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

From Natera, Inc., SCV001465822.1

#	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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002047708.1

#	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: Sep 29, 2024

ClinVar

Relating variation to medicine