NM_000093.5(COL5A1):c.4906G>A (p.Ala1636Thr) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Jun 16, 2022
Review status:: criteria provided, conflicting classifications

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:: RCV000724954.20

Allele description [Variation Report for NM_000093.5(COL5A1):c.4906G>A (p.Ala1636Thr)]

NM_000093.5(COL5A1):c.4906G>A (p.Ala1636Thr)

Genes:

COL5A1:collagen type V alpha 1 chain [Gene - OMIM - HGNC]
LOC101448202:uncharacterized LOC101448202 [Gene]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.3

Genomic location:

Preferred name:

NM_000093.5(COL5A1):c.4906G>A (p.Ala1636Thr)

Other names:

p.A1636T:GCC>ACC

HGVS:

NC_000009.12:g.134824807G>A
NG_008030.1:g.188002G>A
NM_000093.5:c.4906G>AMANE SELECT
NM_001278074.1:c.4906G>A
NP_000084.3:p.Ala1636Thr
NP_000084.3:p.Ala1636Thr
NP_001265003.1:p.Ala1636Thr
LRG_737t1:c.4906G>A
LRG_737t2:c.4906G>A
LRG_737:g.188002G>A
LRG_737p1:p.Ala1636Thr
LRG_737p2:p.Ala1636Thr
NC_000009.11:g.137716653G>A
NM_000093.3:c.4906G>A
NM_000093.4:c.4906G>A
p.Ala1636Thr

Protein change:

A1636T

Links:

dbSNP: rs113452150

NCBI 1000 Genomes Browser:

rs113452150

Molecular consequence:

NM_000093.5:c.4906G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001278074.1:c.4906G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

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
SCV000249921	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Jul 30, 2020)	germline	clinical testing	Citation Link,
SCV000332706	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (Sep 2, 2016)	germline	clinical testing	Citation Link,
SCV001716054	Mayo Clinic Laboratories, Mayo Clinic	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jun 16, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 29924831, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000249921

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Jul 30, 2020)

germline

clinical testing

Citation Link,

SCV000332706

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions 2015)

Uncertain significance
(Sep 2, 2016)

germline

clinical testing

Citation Link,

SCV001716054

Mayo Clinic Laboratories, Mayo Clinic

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jun 16, 2022)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	6	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Rare, potentially pathogenic variants in 21 keratoconus candidate genes are not enriched in cases in a large Australian cohort of European descent.

Lucas SEM, Zhou T, Blackburn NB, Mills RA, Ellis J, Leo P, Souzeau E, Ridge B, Charlesworth JC, Lindsay R, Craig JE, Burdon KP.

PLoS One. 2018;13(6):e0199178. doi: 10.1371/journal.pone.0199178.

PubMed [citation]

PMID:: 29924831
PMCID:: PMC6010250

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, SCV000249921.13

#	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 associated with the following publications: (PMID: 29924831)

#	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 Eurofins Ntd Llc (ga), SCV000332706.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	not provided

#	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		3	not provided	not provided	not provided

From Mayo Clinic Laboratories, Mayo Clinic, SCV001716054.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	not provided	not provided	clinical testing	PubMed (2)

Description

BS1, PP3

#	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		3	not provided	not provided	not provided

Last Updated: Apr 15, 2024

ClinVar

Relating variation to medicine