NM_000090.4(COL3A1):c.3774C>T (p.Pro1258=) AND Familial thoracic aortic aneurysm and aortic dissection

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Nov 27, 2018
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:: RCV001178581.11

Allele description [Variation Report for NM_000090.4(COL3A1):c.3774C>T (p.Pro1258=)]

NM_000090.4(COL3A1):c.3774C>T (p.Pro1258=)

Gene:

COL3A1:collagen type III alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q32.2

Genomic location:

Preferred name:

NM_000090.4(COL3A1):c.3774C>T (p.Pro1258=)

HGVS:

NC_000002.12:g.189009172C>T
NG_007404.1:g.39800C>T
NM_000090.4:c.3774C>TMANE SELECT
NP_000081.1:p.Pro1258=
NP_000081.2:p.Pro1258=
LRG_3t1:c.3774C>T
LRG_3:g.39800C>T
LRG_3p1:p.Pro1258=
NC_000002.11:g.189873898C>T
NM_000090.3:c.3774C>T

Links:

dbSNP: rs149790711

NCBI 1000 Genomes Browser:

rs149790711

Molecular consequence:

NM_000090.4:c.3774C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Familial thoracic aortic aneurysm and aortic dissection (TAAD)
Synonyms:: Thoracic aortic aneurysm and aortic dissection; Thoracic aortic aneurysms and dissections
Identifiers:: MONDO: MONDO:0019625; MedGen: C4707243; Orphanet: 91387; OMIM: PS607086

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Xenopus laevis hypothetical protein MGC64560, mRNA (cDNA clone MGC:64560 IMAGE:6...
Xenopus laevis hypothetical protein MGC64560, mRNA (cDNA clone MGC:64560 IMAGE:6880194), complete cds
gi|32484266|gb|BC054301.1|

Nucleotide
INTS4 integrator complex subunit 4 [Homo sapiens]
INTS4 integrator complex subunit 4 [Homo sapiens]
Gene ID:92105

Gene
92105[uid] AND (alive[prop]) (1)
Gene
xl11010A10R_1374742 Xenopus ORFeome version 1.0 library Xenopus laevis cDNA clon...
xl11010A10R_1374742 Xenopus ORFeome version 1.0 library Xenopus laevis cDNA clone xl11010A10 3', mRNA sequence
gi|798025886|gnl|dbEST|79646877|gb| 175.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000738398	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (Sep 9, 2015)	germline	clinical testing	Citation Link,
SCV001343057	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Nov 27, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000738398

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Benign
(Sep 9, 2015)

germline

clinical testing

Citation Link,

SCV001343057

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Nov 27, 2018)

germline

clinical testing

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

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

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 Ambry Genetics, SCV000738398.5

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

Description

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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 Color Diagnostics, LLC DBA Color Health, SCV001343057.1

#	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

Last Updated: Nov 10, 2024

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