NM_033380.3(COL4A5):c.2858G>T (p.Gly953Val) AND not specified

Germline classification:: Benign (3 submissions)
Last evaluated:: Oct 28, 2019
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:: RCV000598479.10

Allele description [Variation Report for NM_033380.3(COL4A5):c.2858G>T (p.Gly953Val)]

NM_033380.3(COL4A5):c.2858G>T (p.Gly953Val)

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.2858G>T (p.Gly953Val)

HGVS:

NC_000023.11:g.108622766G>T
NG_011977.2:g.187843G>T
NM_000495.5:c.2858G>T
NM_033380.3:c.2858G>TMANE SELECT
NP_000486.1:p.Gly953Val
NP_203699.1:p.Gly953Val
NP_203699.1:p.Gly953Val
LRG_232t1:c.2858G>T
LRG_232t2:c.2858G>T
LRG_232:g.187843G>T
LRG_232p1:p.Gly953Val
LRG_232p2:p.Gly953Val
NC_000023.10:g.107865996G>T
NG_011977.1:g.187843G>T
NM_000495.3:c.2858G>T
NM_000495.4:c.2858G>T
NM_033380.1:c.2858G>T
NM_033380.2:c.2858G>T
P29400:p.Gly953Val

Protein change:

G953V

Links:

UniProtKB: P29400#VAR_011263; dbSNP: rs78972735

NCBI 1000 Genomes Browser:

rs78972735

Molecular consequence:

NM_000495.5:c.2858G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_033380.3:c.2858G>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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
SCV000700762	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Dec 13, 2016)	germline	clinical testing	Citation Link,
SCV000732049	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Dec 21, 2017)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 28827396, 8940267, 25739341, 23967202, 25788563, 27725732, 22995991, 19965530, 24033266
SCV000841178	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Benign (Oct 28, 2019)	unknown	clinical testing	PubMed (18) [See all records that cite these PMIDs] 23967202, 15780079, 25739341, 28827396, 19965530, 25788563, 22995991, 27725732, 22921432, 27627812, 25575550, 18343956, 10561141, 8940267, 31576025, 30577881, 31138263, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000700762

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Benign
(Dec 13, 2016)

germline

clinical testing

Citation Link,

SCV000732049

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Dec 21, 2017)

germline

clinical testing

PubMed (9)
[See all records that cite these PMIDs]

SCV000841178

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Benign
(Oct 28, 2019)

unknown

clinical testing

PubMed (18)
[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	not provided	1	1	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	2	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Targeted exon sequencing successfully discovers rare causative genes and clarifies the molecular epidemiology of Japanese deafness patients.

Miyagawa M, Naito T, Nishio SY, Kamatani N, Usami S.

PLoS One. 2013;8(8):e71381. doi: 10.1371/journal.pone.0071381.

PubMed [citation]

PMID:: 23967202
PMCID:: PMC3742761

See all PubMed Citations (19)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000700762.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	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		2	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000732049.1

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

Description

p.Gly953Val in exon 33 of COL4A5: This variant is not expected to have clinica l significance, because it has been identified in 3.7% (513/13865) of East Asian chromosomes including 7 homozygotes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs104886203, rs78972735). Although it has been reported in several individuals with Alport syndrome or hearing loss, 2 individuals with Alport syndrome had another COL4A5 variant in cis with this va riant, and one individual was reported to have polycystic kidney disease with no additional clinical features of Alport syndrome (Knebelmann 1996, Lennon 2015, Miao 2017, Miyagawa 2013, Nishio 2015, Randles 2016, Tan 2010). In summary, it s frequency is too high to be causative for Alport syndrome. ACMG/AMP criteria a pplied: BA1

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

From Athena Diagnostics, SCV000841178.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (18)

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

Last Updated: Oct 13, 2024

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