NM_004371.4(COPA):c.718T>A (p.Trp240Arg) AND Autoimmune interstitial lung disease-arthritis syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 20, 2019
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:: RCV001201798.7

Allele description

NM_004371.4(COPA):c.718T>A (p.Trp240Arg)

Gene:

COPA:COPI coat complex subunit alpha [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q23.2

Genomic location:

Preferred name:

NM_004371.4(COPA):c.718T>A (p.Trp240Arg)

HGVS:

NC_000001.11:g.160314114A>T
NG_050927.1:g.34451T>A
NM_001098398.2:c.718T>A
NM_004371.4:c.718T>AMANE SELECT
NP_001091868.1:p.Trp240Arg
NP_004362.2:p.Trp240Arg
LRG_1336t1:c.718T>A
LRG_1336:g.34451T>A
LRG_1336p1:p.Trp240Arg
NC_000001.10:g.160283904A>T
NM_004371.3:c.718T>A

Protein change:

W240R

Links:

dbSNP: rs1659063174

NCBI 1000 Genomes Browser:

rs1659063174

Molecular consequence:

NM_001098398.2:c.718T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004371.4:c.718T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Autoimmune interstitial lung disease-arthritis syndrome
Synonyms:: Autoimmune interstitial lung, joint, and kidney disease
Identifiers:: MONDO: MONDO:0014629; MedGen: C5243948; Orphanet: 444092; OMIM: 616414

Recent activity

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nucleotide exchange factor SIL1 precursor [Rattus norvegicus]
nucleotide exchange factor SIL1 precursor [Rattus norvegicus]
gi|40786443|ref|NP_955408.1|

Protein
txid258809[Organism:noexp] (1)
Identical Protein Groups
Pusa caspica cytochrome b gene, complete cds; mitochondrial
Pusa caspica cytochrome b gene, complete cds; mitochondrial
gi|37720380|gb|AY140978.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001372889	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 20, 2019)	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

SCV001372889

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 20, 2019)

germline

clinical testing

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

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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 Invitae, SCV001372889.5

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with COPA-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces tryptophan with arginine at codon 240 of the COPA protein (p.Trp240Arg). The tryptophan residue is highly conserved and there is a moderate physicochemical difference between tryptophan and arginine.

#	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: Feb 28, 2024

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