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NM_000091.4(COL4A3):c.4295G>A (p.Arg1432His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(3);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Aug 10, 2021)
Last evaluated:
Jun 17, 2021
Accession:
VCV000501254.7
Variation ID:
501254
Description:
single nucleotide variant
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NM_000091.4(COL4A3):c.4295G>A (p.Arg1432His)

Allele ID
492678
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
2q36.3
Genomic location
2: 227307752 (GRCh38) GRCh38 UCSC
2: 228172468 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000002.11:g.228172468G>A
NC_000002.12:g.227307752G>A
NM_000091.4:c.4295G>A NP_000082.2:p.Arg1432His missense
... more HGVS
Protein change
R1432H
Other names
-
Canonical SPDI
NC_000002.12:227307751:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00140 (A)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00065
Exome Aggregation Consortium (ExAC) 0.00035
1000 Genomes Project 0.00140
Trans-Omics for Precision Medicine (TOPMed) 0.00100
The Genome Aggregation Database (gnomAD) 0.00076
The Genome Aggregation Database (gnomAD), exomes 0.00033
Links
ClinGen: CA2147500
dbSNP: rs200509072
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000764365.1
Likely benign 1 criteria provided, single submitter Feb 3, 2020 RCV001174854.1
Conflicting interpretations of pathogenicity 3 criteria provided, conflicting interpretations Jun 17, 2021 RCV000597767.5
Likely benign 1 no assertion criteria provided Apr 24, 2020 RCV001276574.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
COL4A3 - - GRCh38
GRCh37
45 1125
MFF-DT - - - GRCh38 - 1062

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Apr 03, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000707547.2
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(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: SCV000895399.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Likely benign
(Feb 03, 2020)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001338244.1
Submitted: (Apr 29, 2020)
Evidence details
Comment:
Variant summary: COL4A3 c.4295G>A (p.Arg1432His) results in a non-conservative amino acid change located in the last collagen triple helix repeat (IPR008160) of the encoded protein … (more)
Likely benign
(Dec 06, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001067203.3
Submitted: (Jan 07, 2021)
Evidence details
Likely benign
(Jun 17, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001778576.1
Submitted: (Aug 10, 2021)
Evidence details
Likely benign
(Apr 24, 2020)
no assertion criteria provided
Method: clinical testing
Autosomal dominant Alport syndrome
Allele origin: germline
Natera, Inc.
Accession: SCV001462973.1
Submitted: (Dec 28, 2020)
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
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
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=COL4A3 - - - -

Text-mined citations for rs200509072...

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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 Aug 17, 2021