NM_001845.6(COL4A1):c.3187C>T (p.Arg1063Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 10, 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:: RCV001938389.3

Allele description [Variation Report for NM_001845.6(COL4A1):c.3187C>T (p.Arg1063Ter)]

NM_001845.6(COL4A1):c.3187C>T (p.Arg1063Ter)

Gene:

COL4A1:collagen type IV alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q34

Genomic location:

Preferred name:

NM_001845.6(COL4A1):c.3187C>T (p.Arg1063Ter)

HGVS:

NC_000013.11:g.110175229G>A
NG_011544.2:g.136921C>T
NM_001845.6:c.3187C>TMANE SELECT
NP_001836.3:p.Arg1063Ter
LRG_1116t1:c.3187C>T
LRG_1116:g.136921C>T
LRG_1116p1:p.Arg1063Ter
NC_000013.10:g.110827576G>A
NM_001845.5:c.3187C>T

Protein change:

R1063*

Links:

dbSNP: rs1877827904

NCBI 1000 Genomes Browser:

rs1877827904

Molecular consequence:

NM_001845.6:c.3187C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV002195600	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 10, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 23225343, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002195600

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 10, 2021)

germline

clinical testing

PubMed (2)
[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

Phenotypic spectrum of COL4A1 mutations: porencephaly to schizencephaly.

Yoneda Y, Haginoya K, Kato M, Osaka H, Yokochi K, Arai H, Kakita A, Yamamoto T, Otsuki Y, Shimizu S, Wada T, Koyama N, Mino Y, Kondo N, Takahashi S, Hirabayashi S, Takanashi J, Okumura A, Kumagai T, Hirai S, Nabetani M, Saitoh S, et al.

Ann Neurol. 2013 Jan;73(1):48-57. doi: 10.1002/ana.23736. Epub 2012 Dec 7.

PubMed [citation]

PMID:: 23225343

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002195600.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant has not been reported in the literature in individuals with COL4A1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Arg1063*) in the COL4A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL4A1 are known to be pathogenic (PMID: 23225343). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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: Aug 18, 2024

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