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NM_000091.5(COL4A3):c.391G>T (p.Glu131Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Jan 7, 2021)
Last evaluated:
Jun 3, 2020
Accession:
VCV000558496.3
Variation ID:
558496
Description:
single nucleotide variant
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NM_000091.5(COL4A3):c.391G>T (p.Glu131Ter)

Allele ID
542010
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q36.3
Genomic location
2: 227246688 (GRCh38) GRCh38 UCSC
2: 228111404 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_230:g.87124G>T
LRG_230t1:c.391G>T LRG_230p1:p.Glu131Ter
NC_000002.11:g.228111404G>T
... more HGVS
Protein change
E131*
Other names
-
Canonical SPDI
NC_000002.12:227246687:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
dbSNP: rs1346138010
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Jun 3, 2020 RCV000674775.2
Pathogenic 1 criteria provided, single submitter Oct 31, 2018 RCV000763077.1
Pathogenic 1 criteria provided, single submitter Mar 31, 2020 RCV001218262.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL4A3 - - GRCh38
GRCh37
47 1197
MFF-DT - - - GRCh38 - 1132

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(May 23, 2018)
criteria provided, single submitter
Method: clinical testing
Alport syndrome, autosomal recessive
Allele origin: unknown
Counsyl
Accession: SCV000800170.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (2)
Pathogenic
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Alport syndrome 3, autosomal dominant
Benign familial hematuria
Alport syndrome, autosomal recessive
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000893589.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Pathogenic
(Jun 03, 2020)
criteria provided, single submitter
Method: clinical testing
Alport syndrome autosomal recessive
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001372411.1
Submitted: (Jul 09, 2020)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: COL4A3 c.391G>T (p.Glu131X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Mar 31, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001390136.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change creates a premature translational stop signal (p.Glu131*) in the COL4A3 gene. It is expected to result in an absent or disrupted protein … (more)

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
Genetic, Clinical, and Pathologic Backgrounds of Patients with Autosomal Dominant Alport Syndrome. Kamiyoshi N Clinical journal of the American Society of Nephrology : CJASN 2016 PMID: 27281700
Identification of 47 novel mutations in patients with Alport syndrome and thin basement membrane nephropathy. Weber S Pediatric nephrology (Berlin, Germany) 2016 PMID: 26809805
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 Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Improving mutation screening in familial hematuric nephropathies through next generation sequencing. Morinière V Journal of the American Society of Nephrology : JASN 2014 PMID: 24854265
COL4A3/COL4A4 mutations and features in individuals with autosomal recessive Alport syndrome. Storey H Journal of the American Society of Nephrology : JASN 2013 PMID: 24052634
Structure of the human type IV collagen gene COL4A3 and mutations in autosomal Alport syndrome. Heidet L Journal of the American Society of Nephrology : JASN 2001 PMID: 11134255
Collagen COL4A3 knockout: a mouse model for autosomal Alport syndrome. Cosgrove D Genes & development 1996 PMID: 8956999

Text-mined citations for rs1346138010...

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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 Oct 30, 2021