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NM_000092.4(COL4A4):c.2630G>A (p.Arg877Gln)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(5);Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
7 (Most recent: Jan 7, 2021)
Last evaluated:
Dec 8, 2020
Accession:
VCV000255023.7
Variation ID:
255023
Description:
single nucleotide variant
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NM_000092.4(COL4A4):c.2630G>A (p.Arg877Gln)

Allele ID
250603
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q36.3
Genomic location
2: 227056031 (GRCh38) GRCh38 UCSC
2: 227920747 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.227920747C>T
NC_000002.12:g.227056031C>T
NM_000092.4:c.2630G>A NP_000083.3:p.Arg877Gln missense
... more HGVS
Protein change
R877Q
Other names
-
Canonical SPDI
NC_000002.12:227056030:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00519 (T)

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00326
Exome Aggregation Consortium (ExAC) 0.00417
Trans-Omics for Precision Medicine (TOPMed) 0.00344
1000 Genomes Project 0.00519
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00263
The Genome Aggregation Database (gnomAD), exomes 0.00383
Links
ClinGen: CA2144755
dbSNP: rs150979437
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign/Likely benign 3 criteria provided, multiple submitters, no conflicts Mar 9, 2018 RCV000241593.4
Benign 2 criteria provided, multiple submitters, no conflicts Dec 8, 2020 RCV000885126.4
Benign 1 criteria provided, single submitter Jan 12, 2018 RCV000364192.2
Uncertain significance 1 criteria provided, single submitter Mar 11, 2020 RCV001089932.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL4A4 - - GRCh38
GRCh37
1176 1201

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(-)
criteria provided, single submitter
Method: clinical testing
NOT SPECIFIED
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000302104.1
Submitted: (Apr 28, 2016)
Evidence details
Likely benign
(Mar 09, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000718721.1
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Oct 26, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Athena Diagnostics Inc
Accession: SCV001143233.1
Submitted: (Sep 25, 2019)
Evidence details
Publications
PubMed (3)
Uncertain significance
(Mar 11, 2020)
criteria provided, single submitter
Method: clinical testing
Alport syndrome, autosomal recessive
Allele origin: germline
Medical Genetics, University of Parma
Accession: SCV001245133.1
Submitted: (Mar 11, 2020)
Evidence details
Benign
(Jan 12, 2018)
criteria provided, single submitter
Method: clinical testing
Alport syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000428094.3
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Benign
(Mar 21, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine
Accession: SCV001365647.1
Submitted: (May 14, 2020)
Evidence details
Comment:
p.Arg877Gln in exon 30 of COL4A4: This variant is not expected to have clinical significance because it has been identified in 2.43% (208/8574) of East … (more)
Benign
(Dec 08, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001028554.3
Submitted: (Jan 07, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Urine-derived podocytes-lineage cells: A promising tool for precision medicine in Alport Syndrome. Daga S Human mutation 2018 PMID: 29098738
Nine novel COL4A3 and COL4A4 mutations and polymorphisms identified in inherited membrane diseases. Rana K Pediatric nephrology (Berlin, Germany) 2007 PMID: 17216251
COL4A3/COL4A4 mutations: from familial hematuria to autosomal-dominant or recessive Alport syndrome. Longo I Kidney international 2002 PMID: 12028435

Text-mined citations for rs150979437...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jul 07, 2021