NM_033380.3(COL4A5):c.2604del (p.Gly869fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 24, 2017
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:: RCV000519538.1

Allele description [Variation Report for NM_033380.3(COL4A5):c.2604del (p.Gly869fs)]

NM_033380.3(COL4A5):c.2604del (p.Gly869fs)

Gene:

COL4A5:collagen type IV alpha 5 chain [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xq22.3

Genomic location:

Preferred name:

NM_033380.3(COL4A5):c.2604del (p.Gly869fs)

HGVS:

NC_000023.11:g.108620353del
NG_011977.2:g.185430del
NM_000495.5:c.2604del
NM_033380.3:c.2604delMANE SELECT
NP_000486.1:p.Gly869fs
NP_203699.1:p.Gly869fs
LRG_232t1:c.2604del
LRG_232t2:c.2604del
LRG_232:g.185430del
LRG_232p1:p.Gly869fs
LRG_232p2:p.Gly869fs
NC_000023.10:g.107863583del
NG_011977.1:g.185430del
NM_033380.1:c.2604delC

Protein change:

G869fs

Links:

dbSNP: rs1556419850

NCBI 1000 Genomes Browser:

rs1556419850

Molecular consequence:

NM_000495.5:c.2604del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_033380.3:c.2604del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000619617	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Jul 24, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000619617

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Jul 24, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000619617.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.2604delC variant in the COL4A5 gene causes a frameshift starting with codon Glycine 869, changes this amino acid to a Glutamic acid residue and creates a premature Stop codon at position 6 of the new reading frame, denoted p.Gly869GlufsX6. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). Although this variant has not been previously reported to our knowledge, we consider ti to be pathogenic.

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

Last Updated: Aug 5, 2023

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