NM_033380.3(COL4A5):c.4063del (p.Glu1355fs) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Aug 31, 2020
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000518573.7

Allele description [Variation Report for NM_033380.3(COL4A5):c.4063del (p.Glu1355fs)]

NM_033380.3(COL4A5):c.4063del (p.Glu1355fs)

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.4063del (p.Glu1355fs)

HGVS:

NC_000023.11:g.108680932del
NG_011977.2:g.246009del
NM_000495.5:c.4045del
NM_033380.3:c.4063delMANE SELECT
NP_000486.1:p.Glu1349fs
NP_203699.1:p.Glu1355fs
LRG_232t1:c.4045del
LRG_232t2:c.4063del
LRG_232:g.246009del
LRG_232p1:p.Glu1349fs
LRG_232p2:p.Glu1355fs
NC_000023.10:g.107924158del
NC_000023.10:g.107924162del
NG_011977.1:g.246009del

Protein change:

E1349fs

Links:

dbSNP: rs1556453276

NCBI 1000 Genomes Browser:

rs1556453276

Molecular consequence:

NM_000495.5:c.4045del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_033380.3:c.4063del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000612994	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Apr 26, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001580932	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 31, 2020)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 9195222, 10752524, 14514738, 24854265, 26809805, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000612994

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Pathogenic
(Apr 26, 2017)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001580932

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 31, 2020)

germline

clinical testing

PubMed (6)
[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

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

The clinical spectrum of type IV collagen mutations.

Lemmink HH, Schröder CH, Monnens LA, Smeets HJ.

Hum Mutat. 1997;9(6):477-99. Review.

PubMed [citation]

PMID:: 9195222

See all PubMed Citations (7)

Details of each submission

From Athena Diagnostics, SCV000612994.1

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

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001580932.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This sequence change creates a premature translational stop signal (p.Glu1349Asnfs*22) in the COL4A5 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with COL4A5-related conditions. ClinVar contains an entry for this variant (Variation ID: 447210). Loss-of-function variants in COL4A5 are known to be pathogenic (PMID: 9195222, 10752524, 14514738, 24854265, 26809805). 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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