NM_000093.5(COL5A1):c.5326T>C (p.Tyr1776His) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 8, 2021
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:: RCV001759559.14

Allele description [Variation Report for NM_000093.5(COL5A1):c.5326T>C (p.Tyr1776His)]

NM_000093.5(COL5A1):c.5326T>C (p.Tyr1776His)

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.5326T>C (p.Tyr1776His)

HGVS:

NC_000009.12:g.134835160T>C
NG_008030.1:g.198355T>C
NM_000093.5:c.5326T>CMANE SELECT
NM_001278074.1:c.5326T>C
NP_000084.3:p.Tyr1776His
NP_000084.3:p.Tyr1776His
NP_001265003.1:p.Tyr1776His
LRG_737t1:c.5326T>C
LRG_737t2:c.5326T>C
LRG_737:g.198355T>C
LRG_737p1:p.Tyr1776His
LRG_737p2:p.Tyr1776His
NC_000009.11:g.137727006T>C
NM_000093.3:c.5326T>C
NM_000093.4:c.5326T>C

Protein change:

Y1776H

Links:

dbSNP: rs778249693

NCBI 1000 Genomes Browser:

rs778249693

Molecular consequence:

NM_000093.5:c.5326T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001278074.1:c.5326T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Homo sapiens actin-related protein T2 (ACTRT2) mRNA, complete cds
Homo sapiens actin-related protein T2 (ACTRT2) mRNA, complete cds
gi|19880696|gb|AF440740.1|

Nucleotide

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
SCV002005243	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Mar 5, 2019)	germline	clinical testing	Citation Link,
SCV002048119	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2021)	Uncertain significance (Oct 8, 2021)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002005243

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Mar 5, 2019)

germline

clinical testing

Citation Link,

SCV002048119

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)

Uncertain significance
(Oct 8, 2021)

germline

clinical testing

Citation Link

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

Details of each submission

From GeneDx, SCV002005243.2

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

Description

In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; Is not located in the triple helical region, where the majority of pathogenic missense variants occur (Stenson et al., 2014).

#	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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002048119.1

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

Description

The COL5A1 c.5326T>C; p.Tyr1776His variant (rs778249693), to our knowledge, is not reported in the medical literature but is reported in the ClinVar database (Variation ID: 653937). The variant is found in the South Asian population with an allele frequency of 0.05% (15/30,614 alleles) in the Genome Aggregation Database. The tyrosine at codon 1776 is highly conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.232). Due to limited information, the clinical significance of the p.Tyr1776His variant is uncertain at this time.

#	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: Oct 13, 2024

ClinVar

Relating variation to medicine