NM_033380.3(COL4A5):c.3230del (p.Gly1077fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 28, 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:: RCV001972737.3

Allele description [Variation Report for NM_033380.3(COL4A5):c.3230del (p.Gly1077fs)]

NM_033380.3(COL4A5):c.3230del (p.Gly1077fs)

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.3230del (p.Gly1077fs)

HGVS:

NC_000023.11:g.108626333del
NG_011977.2:g.191410del
NM_000495.5:c.3230del
NM_033380.3:c.3230delMANE SELECT
NP_000486.1:p.Gly1077fs
NP_203699.1:p.Gly1077fs
LRG_232t1:c.3230del
LRG_232t2:c.3230del
LRG_232:g.191410del
LRG_232p1:p.Gly1077fs
LRG_232p2:p.Gly1077fs
NC_000023.10:g.107869562del
NC_000023.10:g.107869563del

Protein change:

G1077fs

Links:

dbSNP: rs2147873472

NCBI 1000 Genomes Browser:

rs2147873472

Molecular consequence:

NM_000495.5:c.3230del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_033380.3:c.3230del - 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
SCV002240280	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 28, 2021)	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

SCV002240280

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 28, 2021)

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

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

X-linked Alport syndrome: natural history in 195 families and genotype- phenotype correlations in males.

Jais JP, Knebelmann B, Giatras I, Marchi M, Rizzoni G, Renieri A, Weber M, Gross O, Netzer KO, Flinter F, Pirson Y, Verellen C, Wieslander J, Persson U, Tryggvason K, Martin P, Hertz JM, Schröder C, Sanak M, Krejcova S, Carvalho MF, Saus J, et al.

J Am Soc Nephrol. 2000 Apr;11(4):649-657. doi: 10.1681/ASN.V114649.

PubMed [citation]

PMID:: 10752524

See all PubMed Citations (6)

Details of each submission

From Invitae, SCV002240280.3

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

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with COL4A5-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gly1077Valfs*75) in the COL4A5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL4A5 are known to be pathogenic (PMID: 9195222, 10752524, 14514738, 24854265, 26809805).

#	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: Feb 28, 2024

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