NM_033380.3(COL4A5):c.4309C>G (p.Gln1437Glu) AND not specified

Germline classification:: Benign (1 submission)
Last evaluated:: Dec 16, 2021
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:: RCV004017764.1

Allele description [Variation Report for NM_033380.3(COL4A5):c.4309C>G (p.Gln1437Glu)]

NM_033380.3(COL4A5):c.4309C>G (p.Gln1437Glu)

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.4309C>G (p.Gln1437Glu)

HGVS:

NC_000023.11:g.108686123C>G
NG_011977.2:g.251200C>G
NM_000495.5:c.4291C>G
NM_033380.3:c.4309C>GMANE SELECT
NP_000486.1:p.Gln1431Glu
NP_203699.1:p.Gln1437Glu
LRG_232t1:c.4291C>G
LRG_232t2:c.4309C>G
LRG_232:g.251200C>G
LRG_232p1:p.Gln1431Glu
LRG_232p2:p.Gln1437Glu
NC_000023.10:g.107929353C>G
NG_011977.1:g.251200C>G
NM_000495.3:c.4291C>G
NM_000495.4:c.4291C>G
NM_033380.1:c.4309C>G

Protein change:

Q1431E

Links:

dbSNP: rs143778018

NCBI 1000 Genomes Browser:

rs143778018

Molecular consequence:

NM_000495.5:c.4291C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_033380.3:c.4309C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004848606	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Dec 16, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 30295827, 28780565, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004848606

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Dec 16, 2021)

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

Panel sequencing distinguishes monogenic forms of nephritis from nephrosis in children.

Schapiro D, Daga A, Lawson JA, Majmundar AJ, Lovric S, Tan W, Warejko JK, Fessi I, Rao J, Airik M, Gee HY, Schneider R, Widmeier E, Hermle T, Ashraf S, Jobst-Schwan T, van der Ven AT, Nakayama M, Shril S, Braun DA, Hildebrandt F.

Nephrol Dial Transplant. 2019 Mar 1;34(3):474-485. doi: 10.1093/ndt/gfy050.

PubMed [citation]

PMID:: 30295827
PMCID:: PMC6399484

Clinical genetic testing using a custom-designed steroid-resistant nephrotic syndrome gene panel: analysis and recommendations.

Sen ES, Dean P, Yarram-Smith L, Bierzynska A, Woodward G, Buxton C, Dennis G, Welsh GI, Williams M, Saleem MA.

J Med Genet. 2017 Dec;54(12):795-804. doi: 10.1136/jmedgenet-2017-104811. Epub 2017 Aug 5.

PubMed [citation]

PMID:: 28780565
PMCID:: PMC5740557

See all PubMed Citations (3)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV004848606.1

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

Description

The p.Gln1437Glu variant in COL4A5 has been reported in one male Filipino individual with hematuria and proteinuria onset at 1 year old (Schapiro 2019 PMID: 30295827). However, it has also been identified in 0.1154% (17/14727) of East Asian chromosomes by gnomAD (http://gnomad.broadinstitute.org) including 1 homozygote and 1 hemizygote individuals, as well as 2 hemizygotes in other ethnicities. This variant has also been reported in ClinVar (Variation ID 774123). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, the variant is benign based on it's frequency and presence in hemizygous and homozygous individuals in the general population. ACMG/AMP Criteria applied: BA1

#	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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