U.S. flag

An official website of the United States government

NM_033380.3(COL4A5):c.5048G>A (p.Arg1683Gln) AND X-linked Alport syndrome

Germline classification:
Pathogenic/Likely pathogenic (8 submissions)
Last evaluated:
Sep 2, 2022
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:
RCV000011213.18

Allele description [Variation Report for NM_033380.3(COL4A5):c.5048G>A (p.Arg1683Gln)]

NM_033380.3(COL4A5):c.5048G>A (p.Arg1683Gln)

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.5048G>A (p.Arg1683Gln)
HGVS:
  • NC_000023.11:g.108696350G>A
  • NG_011977.2:g.261427G>A
  • NM_000495.5:c.5030G>A
  • NM_033380.3:c.5048G>AMANE SELECT
  • NP_000486.1:p.Arg1677Gln
  • NP_203699.1:p.Arg1683Gln
  • LRG_232t1:c.5030G>A
  • LRG_232t2:c.5048G>A
  • LRG_232:g.261427G>A
  • LRG_232p1:p.Arg1677Gln
  • LRG_232p2:p.Arg1683Gln
  • NC_000023.10:g.107939580G>A
  • NG_011977.1:g.261427G>A
  • NM_000495.3:c.5030G>A
  • NM_000495.4:c.5030G>A
  • NM_000495.5:c.5030G>A
  • NM_033380.1:c.5048G>A
  • NM_033380.2:c.5048G>A
  • P29400:p.Arg1677Gln
  • p.ARG1683GLN
Protein change:
R1677Q; ARG1677GLN
Links:
UniProtKB: P29400#VAR_001974; OMIM: 303630.0015; dbSNP: rs104886308
NCBI 1000 Genomes Browser:
rs104886308
Molecular consequence:
  • NM_000495.5:c.5030G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_033380.3:c.5048G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

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

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000031440OMIM
no assertion criteria provided
Pathogenic
(Jun 1, 2003)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000057826GeneReviews
no classification provided
not providedunknownliterature only

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

SCV000925849Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare
no assertion criteria provided
Pathogenic
(Feb 13, 2019)
germlineclinical testing

SCV001439915Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 1, 2019)
unknownclinical testing

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

SCV001752777Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Feb 6, 2022)
unknownclinical testing

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

SCV002103517Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Feb 18, 2022)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link,

SCV002580335MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Oct 20, 2021)
germlineclinical testing

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

SCV002767563Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 2, 2022)
germlineclinical testing

PubMed (10)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownnot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Immunohistochemical and molecular genetic evidence for type IV collagen alpha5 chain abnormality in the anterior lenticonus associated with Alport syndrome.

Ohkubo S, Takeda H, Higashide T, Ito M, Sakurai M, Shirao Y, Yanagida T, Oda Y, Sado Y.

Arch Ophthalmol. 2003 Jun;121(6):846-50.

PubMed [citation]
PMID:
12796257

Alport Syndrome.

Kashtan CE.

2001 Aug 28 [updated 2019 Feb 21]. In: Adam MP, Feldman J, Mirzaa GM, Pagon RA, Wallace SE, Bean LJH, Gripp KW, Amemiya A, editors. GeneReviews(®) [Internet]. Seattle (WA): University of Washington, Seattle; 1993-2024.

PubMed [citation]
PMID:
20301386
See all PubMed Citations (14)

Details of each submission

From OMIM, SCV000031440.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Nearly all cases of Alport syndrome (ALS1; 301050) involve distinct mutations, as expected for an X-linked disease that significantly reduces the fitness of affected males. A few COL4A5 mutations appear to be associated with reduced disease severity and may account for an appreciable proportion of late-onset Alport syndrome in populations where a founder effect has occurred. Barker et al. (1997) reported a novel mutation in the COL4A5 gene, R1677Q. It was detected in 3 independently ascertained Ashkenazi-American families, caused a relatively mild form of nephritis with typical onset in the fourth or fifth decade, and may be involved in the etiology of a large proportion of adult-onset hereditary nephritis in Ashkenazi Jews. The mutation was a G-to-A transition in nucleotide 5232 and represented a change at a CpG dinucleotide. The same haplotype of COL4A5-linked markers was found in affected males of the 3 kindreds. No genealogic connection could be established.

Ohkubo et al. (2003) found immunohistochemical evidence that the normal anterior lens capsule expressed all of the A4 collagen chains. They also examined the anterior lens capsule of a patient with Alport syndrome due to the R1677X nonsense mutation. The patient's anterior lenticonus resulted in a lack of immunoreactivity to 4A3 to 4A6 chains in the anterior lens capsule.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From GeneReviews, SCV000057826.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownnot providednot providednot providedAssert pathogenicitynot providednot providednot providednot provided

From Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare, SCV000925849.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001439915.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV001752777.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002103517.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: COL4A5 c.5030G>A (p.Arg1677Gln) results in a conservative amino acid change located in the Collagen IV, non-collagenous domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2.2e-05 in 183310 control chromosomes. c.5030G>A has been reported in the literature in multiple individuals affected with Alport Syndrome 1, X-Linked Recessive or Nephrosclerosis/deafness (e.g. Bekheirnia_2010, Ottlewski_2019). These data indicate that the variant is very likely to be associated with disease. Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From MGZ Medical Genetics Center, SCV002580335.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002767563.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (10)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative and loss of function are known mechanisms of disease in this gene and are associated with X-linked Alport syndrome 1 (MIM#301050). Dominant negative is caused mostly glycine substitutions that affect the conformation of the protein, and loss of function can be caused by either protein truncating or missense variants (PMID: 24046192, PMID: 12028435). (I) 0110 - This gene is known to be associated with X-linked dominant disease. Males are typically more severely affected than females (PMID: 19965530). (I) 0115 - Variants in this gene are known to have variable expressivity. There is intrafamilial variability among affected carrier females, possibly due to variable X-inactivation (PMID: 14514738). (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to glutamine. (I) 0253 - Variant is hemizygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (4 heterozygotes, 0 homozygotes, 0 hemizygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools and highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the C-terminal tandem repeated domain in type 4 collagen (NCBI conserved domain). (I) 0703 - Other missense variants comparable to the one identified in this case have moderate previous evidence for pathogenicity. The p.(Arg1677Pro) and p.(Arg1677Leu) comparable variants have each been reported in an individual with Alport Syndrome, respectively (PMIDs: 11223851; 21505094). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant is an Ashkenazi Jewish founder mutation and has been classified as pathogenic in ClinVar (PMIDs: 9150741; 27627812). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. HEK293T cells carrying the p.(Arg1683Gln) mutant construct demonstrated impaired trimer formation ability with alpha-3 and alpha-4 collagen chains compared with the wild type construct (PMID: 29526710). (SP) 1102 - Strong phenotype match. (SP) 1208 - Inheritance information for this variant is not currently available. (I) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 12, 2024