NM_033380.3(COL4A5):c.515del (p.Asn172fs) AND X-linked Alport syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 27, 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:: RCV002310054.2

Allele description [Variation Report for NM_033380.3(COL4A5):c.515del (p.Asn172fs)]

NM_033380.3(COL4A5):c.515del (p.Asn172fs)

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.515del (p.Asn172fs)

HGVS:

NC_000023.11:g.108573623del
NG_011977.2:g.138700del
NM_000495.5:c.515del
NM_033380.3:c.515delMANE SELECT
NP_000486.1:p.Asn172fs
NP_203699.1:p.Asn172fs
LRG_232t1:c.515del
LRG_232t2:c.515del
LRG_232:g.138700del
LRG_232p1:p.Asn172fs
LRG_232p2:p.Asn172fs
NC_000023.10:g.107816853del

Protein change:

N172fs

Molecular consequence:

NM_000495.5:c.515del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_033380.3:c.515del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: X-linked Alport syndrome (ATS1)
Synonyms:: NEPHROPATHY AND DEAFNESS, X-LINKED; Alport syndrome 1, X-linked recessive; Alport Syndrome and Thin Basement Membrane Nephropathy
Identifiers:: MONDO: MONDO:0010520; MedGen: C4746986; Orphanet: 63; Orphanet: 88917; OMIM: 301050

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002604305	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))	Likely pathogenic (Feb 27, 2022)	unknown	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002604305

Myriad Genetics, Inc.

criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2021))

Likely pathogenic
(Feb 27, 2022)

unknown

clinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Myriad Genetics, Inc., SCV002604305.2

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

Description

NM_000495.4(COL4A5):c.515delA(N172Ifs*31) is expected to be pathogenic in the context of X-linked Alport syndrome. This variant is predicted to lead to an abnormal or absent protein product due to the creation of a premature termination codon in COL4A5, a gene where loss-of-function variants are known to be pathogenic. Please note: this variant was assessed in the context of healthy population screening.

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

Last Updated: Aug 5, 2023

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