NM_000094.4(COL7A1):c.6248C>T (p.Thr2083Ile) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 11, 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:: RCV002715057.2

Allele description [Variation Report for NM_000094.4(COL7A1):c.6248C>T (p.Thr2083Ile)]

NM_000094.4(COL7A1):c.6248C>T (p.Thr2083Ile)

Gene:

COL7A1:collagen type VII alpha 1 chain [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.31

Genomic location:

Preferred name:

NM_000094.4(COL7A1):c.6248C>T (p.Thr2083Ile)

HGVS:

NC_000003.12:g.48575095G>A
NG_007065.1:g.25158C>T
NM_000094.4:c.6248C>TMANE SELECT
NP_000085.1:p.Thr2083Ile
NP_000085.1:p.Thr2083Ile
LRG_286t1:c.6248C>T
LRG_286:g.25158C>T
LRG_286p1:p.Thr2083Ile
NC_000003.11:g.48612528G>A
NM_000094.3:c.6248C>T

Protein change:

T2083I

Molecular consequence:

NM_000094.4:c.6248C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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DA997676 T1ESE2 Homo sapiens cDNA clone T1ESE2001663 5', mRNA sequence
gi|82052142|gnl|dbEST|33687338|dbj| 676.1|

Nucleotide
Ophioderma panamensis voucher CE-UAM 683 cytochrome c oxidase subunit I (COX1) g...
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gi|2619206751|gb|OR789595.1|

Nucleotide
RNA-seq analysis of gene expression in macrophages progenitors from the yolk sac...
RNA-seq analysis of gene expression in macrophages progenitors from the yolk sac of murine embryos at embryonic days 9 and 10, and the modifications resulting from a defective expression of the transcription factor Lyl-1
RNA-seq analysis of gene expression in macrophages progenitors from the yolk sac of murine embryos at embryonic days 9 and 10, and the modifications resulting from a defective expression of the transcription factor Lyl-1

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002989478	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 11, 2021)	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

SCV002989478

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 11, 2021)

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002989478.1

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

Description

This sequence change replaces threonine with isoleucine at codon 2083 of the COL7A1 protein (p.Thr2083Ile). The threonine residue is weakly conserved and there is a moderate physicochemical difference between threonine and isoleucine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with COL7A1-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt COL7A1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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