NM_001034850.3(RETREG1):c.22G>A (p.Glu8Lys) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: May 19, 2022
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:: RCV000702166.9

Allele description [Variation Report for NM_001034850.3(RETREG1):c.22G>A (p.Glu8Lys)]

NM_001034850.3(RETREG1):c.22G>A (p.Glu8Lys)

Genes:

LOC129993734:ATAC-STARR-seq lymphoblastoid silent region 15947 [Gene]
RETREG1-AS1:RETREG1 antisense RNA 1 [Gene - HGNC]
RETREG1:reticulophagy regulator 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5p15.1

Genomic location:

Preferred name:

NM_001034850.3(RETREG1):c.22G>A (p.Glu8Lys)

HGVS:

NC_000005.10:g.16616950C>T
NG_016644.2:g.5060G>A
NM_001034850.3:c.22G>AMANE SELECT
NP_001030022.1:p.Glu8Lys
NP_001030022.1:p.Glu8Lys
LRG_363t1:c.22G>A
LRG_363:g.5060G>A
LRG_363p1:p.Glu8Lys
NC_000005.9:g.16617059C>T
NM_001034850.1:c.22G>A
NM_001034850.2:c.22G>A

Protein change:

E8K

Links:

dbSNP: rs759050645

NCBI 1000 Genomes Browser:

rs759050645

Molecular consequence:

NM_001034850.3:c.22G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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MULTISPECIES: 16S rRNA (guanine(1405)-N(7))-methyltransferase ArmA [Gammaproteob...
MULTISPECIES: 16S rRNA (guanine(1405)-N(7))-methyltransferase ArmA [Gammaproteobacteria]
gi|446282131|ref|WP_000359986.1|

Protein
TLS: soil metagenome ribosomal RNA internal transcribed spacer region, targeted ...
TLS: soil metagenome ribosomal RNA internal transcribed spacer region, targeted locus study
gi|2667557326|gb|KDPX00000000.1|KDP 0000

Nucleotide
FAD-dependent oxidoreductase [Arthrobacter flavus]
FAD-dependent oxidoreductase [Arthrobacter flavus]
gi|2729249038|ref|WP_343880310.1|

Protein
AAA family ATPase [Arthrobacter flavus]
AAA family ATPase [Arthrobacter flavus]
gi|2729246736|ref|WP_343878221.1|

Protein
tRNA lysidine(34) synthetase TilS [Stutzerimonas frequens]
tRNA lysidine(34) synthetase TilS [Stutzerimonas frequens]
gi|1783046201|ref|WP_156244555.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000831007	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 19, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002586733	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Apr 21, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000831007

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 19, 2022)

germline

clinical testing

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

SCV002586733

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Apr 21, 2022)

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

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, SCV000831007.6

#	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 glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 8 of the RETREG1 protein (p.Glu8Lys). This variant is present in population databases (rs759050645, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with RETREG1-related conditions. ClinVar contains an entry for this variant (Variation ID: 352697). 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: "Tolerated"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). 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

From GeneDx, SCV002586733.2

#	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 supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; In-silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.

#	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

Last Updated: Sep 29, 2024

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