NM_000090.4(COL3A1):c.1257C>T (p.Ala419=) AND not specified

Germline classification:: Benign (2 submissions)
Last evaluated:: May 20, 2013
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:: RCV000124398.17

Allele description [Variation Report for NM_000090.4(COL3A1):c.1257C>T (p.Ala419=)]

NM_000090.4(COL3A1):c.1257C>T (p.Ala419=)

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.1257C>T (p.Ala419=)

Other names:

p.A419A:GCC>GCT

HGVS:

NC_000002.12:g.188994296C>T
NG_007404.1:g.24924C>T
NM_000090.4:c.1257C>TMANE SELECT
NP_000081.1:p.Ala419=
NP_000081.2:p.Ala419=
LRG_3t1:c.1257C>T
LRG_3:g.24924C>T
LRG_3p1:p.Ala419=
NC_000002.11:g.189859022C>T
NM_000090.3:c.1257C>T

Links:

dbSNP: rs41272837

NCBI 1000 Genomes Browser:

rs41272837

Molecular consequence:

NM_000090.4:c.1257C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

Clear Turn Off Turn On

Molossus molossus isolate mMolMol1 unplaced genomic scaffold, mMolMol1.p scaffol...
Molossus molossus isolate mMolMol1 unplaced genomic scaffold, mMolMol1.p scaffold_m16_p_22, whole genome shotgun sequence
gi|1909389739|gnl|ASM:GCF_014108425 affold_m16_p_22|ref|NW_023425358.1||gpp|GPS_020227796.1|

Nucleotide
BioCollections for Protein (Select 2462632158) (1)
Biocollections
lysine-specific demethylase 5D isoform X8 [Homo sapiens]
lysine-specific demethylase 5D isoform X8 [Homo sapiens]
gi|2462632158|ref|XP_054184348.1|

Protein

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000167831	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Benign (May 20, 2013)	germline	clinical testing	Citation Link,
SCV000302016	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	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

SCV000167831

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Benign
(May 20, 2013)

germline

clinical testing

Citation Link,

SCV000302016

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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 GeneDx, SCV000167831.11

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From PreventionGenetics, part of Exact Sciences, SCV000302016.1

#	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 3, 2024

ClinVar

Relating variation to medicine