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NM_001776.6(ENTPD1):c.656C>T (p.Thr219Ile) AND Hereditary spastic paraplegia 64

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 28, 2022
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:
RCV002650869.2

Allele description

NM_001776.6(ENTPD1):c.656C>T (p.Thr219Ile)

Genes:
ENTPD1-AS1:ENTPD1 antisense RNA 1 [Gene - HGNC]
ENTPD1:ectonucleoside triphosphate diphosphohydrolase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q24.1
Genomic location:
Preferred name:
NM_001776.6(ENTPD1):c.656C>T (p.Thr219Ile)
HGVS:
  • NC_000010.11:g.95845439C>T
  • NG_042803.2:g.156255C>T
  • NM_001098175.2:c.677C>T
  • NM_001164178.1:c.692C>T
  • NM_001164179.2:c.656C>T
  • NM_001164181.1:c.332C>T
  • NM_001164182.2:c.242C>T
  • NM_001164183.2:c.242C>T
  • NM_001312654.1:c.332C>T
  • NM_001320916.1:c.692C>T
  • NM_001776.6:c.656C>TMANE SELECT
  • NP_001091645.1:p.Thr226Ile
  • NP_001157650.1:p.Thr231Ile
  • NP_001157651.1:p.Thr219Ile
  • NP_001157653.1:p.Thr111Ile
  • NP_001157654.1:p.Thr81Ile
  • NP_001157655.1:p.Thr81Ile
  • NP_001299583.1:p.Thr111Ile
  • NP_001307845.1:p.Thr231Ile
  • NP_001767.3:p.Thr219Ile
  • NC_000010.10:g.97605196C>T
  • NG_042803.1:g.138661C>T
Protein change:
T111I
Molecular consequence:
  • NM_001098175.2:c.677C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164178.1:c.692C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164179.2:c.656C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164181.1:c.332C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164182.2:c.242C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001164183.2:c.242C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001312654.1:c.332C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001320916.1:c.692C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001776.6:c.656C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary spastic paraplegia 64
Synonyms:
Spastic paraplegia 64, autosomal recessive
Identifiers:
MONDO: MONDO:0014303; MedGen: C3810289; Orphanet: 401810; OMIM: 615683

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003515576Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 28, 2022) 		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, SCV003515576.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical 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 (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with ENTPD1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 219 of the ENTPD1 protein (p.Thr219Ile).

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

Last Updated: Feb 14, 2024