NC_000023.10:g.(?_107898541)_(107979574_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 11, 2022
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:: RCV003111314.5

Allele description [Variation Report for NC_000023.10:g.(?_107898541)_(107979574_?)del]

NC_000023.10:g.(?_107898541)_(107979574_?)del

Genes:: COL4A5:collagen type IV alpha 5 chain [Gene - OMIM - HGNC]
IRS4:insulin receptor substrate 4 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: Xq22.3
Genomic location:: ChrX: 107898541 - 107979574 (on Assembly GRCh37)
Preferred name:: NC_000023.10:g.(?_107898541)_(107979574_?)del
HGVS:: NC_000023.10:g.(?_107898541)_(107979574_?)del
This HGVS expression did not pass validation

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003793334	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 11, 2022)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 18584212, 7695699, 8218237, 19344236, 23720012, 27627812, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003793334

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 11, 2022)

germline

clinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Detection of large deletion mutations in the COL4A5 gene of female Alport syndrome patients.

Nozu K, Przybyslaw Krol R, Ohtsuka Y, Nakanishi K, Yoshikawa N, Nozu Y, Kaito H, Kanda K, Hashimura Y, Hamasaki Y, Iijima K, Matsuo M.

Pediatr Nephrol. 2008 Nov;23(11):2085-90. doi: 10.1007/s00467-008-0878-y. Epub 2008 Jun 27.

PubMed [citation]

PMID:: 18584212

Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution.

Bella J, Eaton M, Brodsky B, Berman HM.

Science. 1994 Oct 7;266(5182):75-81.

PubMed [citation]

PMID:: 7695699

See all PubMed Citations (7)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003793334.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 37-51 of the COL4A5 gene, which includes the termination codon. This deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. While this deletion is not anticipated to lead to nonsense mediated decay, it is expected to alter mRNA translation or result in a truncated protein product. A similar copy number variant has been observed in individual(s) with Alport syndrome (PMID: 18584212). This variant disrupts the triple helix domain of COL4A5. Glycine residues within the Gly-Xaa-Yaa repeats of the triple helix domain are required for the structure and stability of fibrillar collagens (PMID: 7695699, 8218237, 19344236). In COL4A5, missense variants at these glycine residues are significantly enriched in individuals with disease (PMID: 23720012, 27627812) compared to the general population (ExAC). For these reasons, this variant has been classified as Pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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