NM_000092.5(COL4A4):c.4715C>T (p.Pro1572Leu) AND Alport syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Apr 27, 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:: RCV001140736.9

Allele description [Variation Report for NM_000092.5(COL4A4):c.4715C>T (p.Pro1572Leu)]

NM_000092.5(COL4A4):c.4715C>T (p.Pro1572Leu)

Gene:

COL4A4:collagen type IV alpha 4 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q36.3

Genomic location:

Preferred name:

NM_000092.5(COL4A4):c.4715C>T (p.Pro1572Leu)

HGVS:

NC_000002.12:g.227008112G>A
NG_011592.1:g.161448C>T
NM_000092.5:c.4715C>TMANE SELECT
NP_000083.3:p.Pro1572Leu
NP_000083.3:p.Pro1572Leu
LRG_231t1:c.4715C>T
LRG_231:g.161448C>T
LRG_231p1:p.Pro1572Leu
NC_000002.11:g.227872828G>A
NM_000092.4:c.4715C>T
P53420:p.Pro1572Leu

Protein change:

P1572L; PRO1572LEU

Links:

UniProtKB: P53420#VAR_008155; OMIM: 120131.0006; dbSNP: rs121912863

NCBI 1000 Genomes Browser:

rs121912863

Molecular consequence:

NM_000092.5:c.4715C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Alport syndrome
Synonyms:: Hemorrhagic familial nephritis; Hemorrhagic hereditary nephritis; Congenital hereditary hematuria
Identifiers:: MONDO: MONDO:0018965; MedGen: C1567741; OMIM: PS301050

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001301022	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Uncertain significance (Apr 27, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001301022

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Uncertain significance
(Apr 27, 2017)

germline

clinical testing

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

Citation Link

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, research

Citations

PubMed

Determination of the genomic structure of the COL4A4 gene and of novel mutations causing autosomal recessive Alport syndrome.

Boye E, Mollet G, Forestier L, Cohen-Solal L, Heidet L, Cochat P, Grünfeld JP, Palcoux JB, Gubler MC, Antignac C.

Am J Hum Genet. 1998 Nov;63(5):1329-40.

PubMed [citation]

PMID:: 9792860
PMCID:: PMC1377543

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001301022.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

#	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 Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV002047444.1

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

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002047444	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	flagged submission Reason: Outlier claim with insufficient supporting evidence Notes: None (ACMG Guidelines, 2015)	Likely pathogenic	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002047444

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

flagged submission

Reason: Outlier claim with insufficient supporting evidence

Notes: None

(ACMG Guidelines, 2015)

Likely pathogenic

germline

research

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

Last Updated: Sep 16, 2024

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