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NM_033380.3(COL4A5):c.3107-4A>G AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Apr 9, 2021
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:
RCV001957055.5

Allele description [Variation Report for NM_033380.3(COL4A5):c.3107-4A>G]

NM_033380.3(COL4A5):c.3107-4A>G

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.3107-4A>G
HGVS:
  • NC_000023.11:g.108626206A>G
  • NG_011977.2:g.191283A>G
  • NM_000495.5:c.3107-4A>G
  • NM_033380.3:c.3107-4A>GMANE SELECT
  • LRG_232t1:c.3107-4A>G
  • LRG_232t2:c.3107-4A>G
  • LRG_232:g.191283A>G
  • NC_000023.10:g.107869436A>G
  • NG_011977.1:g.191283A>G
  • NM_000495.4:c.3107-4A>G
Links:
dbSNP: rs397515497
NCBI 1000 Genomes Browser:
rs397515497
Molecular consequence:
  • NM_000495.5:c.3107-4A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_033380.3:c.3107-4A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002252764Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Apr 9, 2021)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Detection of Splicing Abnormalities and Genotype-Phenotype Correlation in X-linked Alport Syndrome.

Horinouchi T, Nozu K, Yamamura T, Minamikawa S, Omori T, Nakanishi K, Fujimura J, Ashida A, Kitamura M, Kawano M, Shimabukuro W, Kitabayashi C, Imafuku A, Tamagaki K, Kamei K, Okamoto K, Fujinaga S, Oka M, Igarashi T, Miyazono A, Sawanobori E, Fujimaru R, et al.

J Am Soc Nephrol. 2018 Aug;29(8):2244-2254. doi: 10.1681/ASN.2018030228. Epub 2018 Jun 29.

PubMed [citation]
PMID:
29959198
PMCID:
PMC6065097

Twenty-one novel mutations identified in the COL4A5 gene in Chinese patients with X-linked Alport's syndrome confirmed by skin biopsy.

Ma J, Pan X, Wang Z, Wang Y, Feng X, Ren H, Zhang W, Chen X, Wang W, Chen N.

Nephrol Dial Transplant. 2011 Dec;26(12):4003-10. doi: 10.1093/ndt/gfr184. Epub 2011 Apr 19.

PubMed [citation]
PMID:
21505094
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002252764.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Studies have shown that this variant is associated with the activation of a cryptic splice site in intron 35 (PMID: 21505094). This variant has been observed in individual(s) with clinical features of Alport syndrome (PMID: 29959198, 21505094). ClinVar contains an entry for this variant (Variation ID: 38773). This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 35 of the COL4A5 gene. It does not directly change the encoded amino acid sequence of the COL4A5 protein. RNA analysis indicates that this variant induces altered splicing and likely results in the gain of one amino acid residue(s), but is expected to preserve the integrity of the reading-frame.

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

Last Updated: Sep 29, 2024