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NM_001845.6(COL4A1):c.343G>A (p.Gly115Ser) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 23, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV003448478.1

Allele description [Variation Report for NM_001845.6(COL4A1):c.343G>A (p.Gly115Ser)]

NM_001845.6(COL4A1):c.343G>A (p.Gly115Ser)

Gene:
COL4A1:collagen type IV alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q34
Genomic location:
Preferred name:
NM_001845.6(COL4A1):c.343G>A (p.Gly115Ser)
HGVS:
  • NC_000013.11:g.110212461C>T
  • NG_011544.2:g.99689G>A
  • NM_001303110.2:c.343G>A
  • NM_001845.6:c.343G>AMANE SELECT
  • NP_001290039.1:p.Gly115Ser
  • NP_001836.3:p.Gly115Ser
  • LRG_1116t1:c.343G>A
  • LRG_1116:g.99689G>A
  • LRG_1116p1:p.Gly115Ser
  • NC_000013.10:g.110864808C>T
Protein change:
G115S
Molecular consequence:
  • NM_001303110.2:c.343G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001845.6:c.343G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Autosomal dominant familial hematuria-retinal arteriolar tortuosity-contractures syndrome
Synonyms:
Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps
Identifiers:
MONDO: MONDO:0012726; MedGen: C2673195; Orphanet: 73229; OMIM: 611773
Name:
Brain small vessel disease 1 with or without ocular anomalies (BSVD1)
Synonyms:
Brain small vessel disease with hemorrhage
Identifiers:
MONDO: MONDO:0008289; MedGen: C4551998; Orphanet: 2940; Orphanet: 99810; OMIM: 175780
Name:
Retinal arterial tortuosity
Synonyms:
RETINAL HEMORRHAGE WITH VASCULAR TORTUOSITY; Retinal arteries, tortuosity of
Identifiers:
MONDO: MONDO:0008373; MedGen: C0423401; Orphanet: 75326; OMIM: 180000; Human Phenotype Ontology: HP:0000631
Name:
Microangiopathy and leukoencephalopathy, pontine, autosomal dominant
Synonyms:
DEMENTIA, HEREDITARY MULTI-INFARCT, SWEDISH TYPE; Pontine autosomal dominant microangiopathy with leukoencephalopathy
Identifiers:
MONDO: MONDO:0032814; MedGen: C5231411; Orphanet: 477749; OMIM: 618564

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004176161New York Genome Center
criteria provided, single submitter

(NYGC Assertion Criteria 2020)		Uncertain significance
(Aug 23, 2023) 		inheritedclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedinheritedunknown1not providednot provided1not providedclinical testing

Details of each submission

From New York Genome Center, SCV004176161.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The inherited c.343G>A, p.(Gly115Ser) variant identified in the COL4A1 gene is a single nucleotide variant that results in the substitution of a well conserved Glycine for Serine at amino acid 115/1670 (exon 6/52) within a Gly-X-Y repeat of the triple-helical region (InterPro:P02462). This variant is found with low frequency in population databases (28 heterozygotes, allele frequency=2.95e-5; gnomADv2.1.1, gnomADv3.1.2, BRAVO-TOPMed, All of Us) suggesting it is not a common benign variant in the populations represented in those databases. In silico algorithms predict this variant to be deleterious to the function of the canonical transcript (REVEL; score=0.96). The c.343G>A, p.(Gly115Ser) variant is reported in ClinVar as Likely Pathogenic (VarID:2158622) and to our current knowledge has not been reported in affected individuals in the literature. Given the available evidence, the inherited c.343G>A, p.(Gly115Ser) variant identified in the COL4A1 gene is reported as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedunknown1not providednot provided1not providednot providednot provided

Last Updated: Oct 20, 2024