NM_001776.6(ENTPD1):c.43A>G (p.Lys15Glu) AND Hereditary spastic paraplegia 64

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 19, 2023
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:: RCV003747421.2

Allele description

NM_001776.6(ENTPD1):c.43A>G (p.Lys15Glu)

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.43A>G (p.Lys15Glu)

HGVS:

NC_000010.11:g.95823263A>G
NG_042803.1:g.116485A>G
NG_042803.2:g.134079A>G
NM_001098175.2:c.64A>G
NM_001164178.1:c.79A>G
NM_001164179.2:c.43A>G
NM_001164181.1:c.-180-16428A>G
NM_001164182.2:c.-221A>G
NM_001164183.2:c.-103A>G
NM_001312654.1:c.-181+12457A>G
NM_001320916.1:c.79A>G
NM_001776.6:c.43A>GMANE SELECT
NP_001091645.1:p.Lys22Glu
NP_001157650.1:p.Lys27Glu
NP_001157651.1:p.Lys15Glu
NP_001307845.1:p.Lys27Glu
NP_001767.3:p.Lys15Glu
NC_000010.10:g.97583020A>G

Protein change:

K15E

Molecular consequence:

NM_001164182.2:c.-221A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001164183.2:c.-103A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001164181.1:c.-180-16428A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001312654.1:c.-181+12457A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001098175.2:c.64A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001164178.1:c.79A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001164179.2:c.43A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001320916.1:c.79A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001776.6:c.43A>G - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004450415	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 19, 2023)	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

SCV004450415

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 19, 2023)

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, SCV004450415.1

#	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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. 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 lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 15 of the ENTPD1 protein (p.Lys15Glu).

#	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: Jun 23, 2024

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