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NM_006459.4(ERLIN1):c.269G>T (p.Arg90Leu) AND Hereditary spastic paraplegia 62

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 17, 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:
RCV001980012.4

Allele description

NM_006459.4(ERLIN1):c.269G>T (p.Arg90Leu)

Gene:
ERLIN1:ER lipid raft associated 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q24.31
Genomic location:
Preferred name:
NM_006459.4(ERLIN1):c.269G>T (p.Arg90Leu)
HGVS:
  • NC_000010.11:g.100178168C>A
  • NG_052910.1:g.12890G>T
  • NM_001100626.2:c.269G>T
  • NM_001347856.2:c.17G>T
  • NM_001347857.2:c.269G>T
  • NM_001347858.2:c.-176-2098G>T
  • NM_001347859.2:c.269G>T
  • NM_001347860.2:c.269G>T
  • NM_001347861.2:c.269G>T
  • NM_006459.4:c.269G>TMANE SELECT
  • NP_001094096.1:p.Arg90Leu
  • NP_001334785.1:p.Arg6Leu
  • NP_001334786.1:p.Arg90Leu
  • NP_001334788.1:p.Arg90Leu
  • NP_001334789.1:p.Arg90Leu
  • NP_001334790.1:p.Arg90Leu
  • NP_006450.2:p.Arg90Leu
  • NC_000010.10:g.101937925C>A
  • NR_144755.2:n.266G>T
  • NR_144756.2:n.348G>T
  • NR_144758.2:n.348G>T
  • NR_144759.2:n.406G>T
  • NR_144760.2:n.511G>T
Protein change:
R6L
Links:
dbSNP: rs779963349
NCBI 1000 Genomes Browser:
rs779963349
Molecular consequence:
  • NM_001347858.2:c.-176-2098G>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001100626.2:c.269G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001347856.2:c.17G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001347857.2:c.269G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001347859.2:c.269G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001347860.2:c.269G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001347861.2:c.269G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006459.4:c.269G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_144755.2:n.266G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144756.2:n.348G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144758.2:n.348G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144759.2:n.406G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_144760.2:n.511G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Hereditary spastic paraplegia 62
Synonyms:
Spastic paraplegia 62, autosomal recessive
Identifiers:
MONDO: MONDO:0014302; MedGen: C4284588; Orphanet: 401785; OMIM: 615681

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002224779Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 17, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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, SCV002224779.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change replaces arginine with leucine at codon 90 of the ERLIN1 protein (p.Arg90Leu). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and leucine. This variant is present in population databases (rs779963349, ExAC 0.05%). This variant has not been reported in the literature in individuals affected with ERLIN1-related conditions. 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: "Probably Damaging"; 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 24, 2023