NM_001351169.2(NT5C2):c.1678GAA[3] (p.Glu561_Ter562insGlu) AND Hereditary spastic paraplegia 45

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 29, 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:: RCV002659167.3

Allele description [Variation Report for NM_001351169.2(NT5C2):c.1678GAA[3] (p.Glu561_Ter562insGlu)]

NM_001351169.2(NT5C2):c.1678GAA[3] (p.Glu561_Ter562insGlu)

Genes:

NT5C2:5'-nucleotidase, cytosolic II [Gene - OMIM - HGNC]
CNNM2:cyclin and CBS domain divalent metal cation transport mediator 2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

10q24.32

Genomic location:

Preferred name:

NM_001351169.2(NT5C2):c.1678GAA[3] (p.Glu561_Ter562insGlu)

HGVS:

NC_000010.11:g.103089675TTC[3]
NG_031932.2:g.176383TTC[3]
NG_042272.1:g.108627GAA[3]
NM_001134373.3:c.1678GAA[3]
NM_001351169.2:c.1678GAA[3]MANE SELECT
NM_001351170.2:c.1702GAA[3]
NM_001351171.2:c.1702GAA[3]
NM_001351172.2:c.1702GAA[3]
NM_001351173.2:c.1702GAA[3]
NM_001351174.1:c.1591GAA[3]
NM_001351175.2:c.1585GAA[3]
NM_001351176.2:c.1105GAA[3]
NM_001351177.2:c.1105GAA[3]
NM_001351178.2:c.1105GAA[3]
NM_001351179.2:c.1105GAA[3]
NM_001351180.2:c.1105GAA[3]
NM_001351181.2:c.1105GAA[3]
NM_001351182.2:c.1105GAA[3]
NM_001351183.2:c.1105GAA[3]
NM_001351184.2:c.1105GAA[3]
NM_001351185.2:c.1105GAA[3]
NM_001351186.2:c.1105GAA[3]
NM_001351187.2:c.1105GAA[3]
NM_001351188.2:c.1105GAA[3]
NM_001351189.2:c.1105GAA[3]
NM_001351190.2:c.1105GAA[3]
NM_001351191.1:c.1105GAA[3]
NM_001351192.1:c.1105GAA[3]
NM_001351193.1:c.1105GAA[3]
NM_001351194.2:c.964GAA[3]
NM_001351195.2:c.964GAA[3]
NM_001351196.2:c.964GAA[3]
NM_001351197.2:c.1105GAA[3]
NM_012229.5:c.1678GAA[3]
NM_017649.5:c.*12495TTC[3]MANE SELECT
NM_199076.3:c.*12495TTC[3]
NP_001127845.1:p.Glu561_Ter562insGlu
NP_001127845.1:p.Glu561_Ter562insGlu
NP_001338098.1:p.Glu561_Ter562insGlu
NP_001338098.1:p.Glu561_Ter562insGlu
NP_001338099.1:p.Glu569_Ter570insGlu
NP_001338099.1:p.Glu569_Ter570insGlu
NP_001338100.1:p.Glu569_Ter570insGlu
NP_001338100.1:p.Glu569_Ter570insGlu
NP_001338101.1:p.Glu569_Ter570insGlu
NP_001338101.1:p.Glu569_Ter570insGlu
NP_001338102.1:p.Glu569_Ter570insGlu
NP_001338102.1:p.Glu569_Ter570insGlu
NP_001338103.1:p.Glu532_Ter533insGlu
NP_001338104.1:p.Glu530_Ter531insGlu
NP_001338104.1:p.Glu530_Ter531insGlu
NP_001338105.1:p.Glu370_Ter371insGlu
NP_001338105.1:p.Glu370_Ter371insGlu
NP_001338106.1:p.Glu370_Ter371insGlu
NP_001338106.1:p.Glu370_Ter371insGlu
NP_001338107.1:p.Glu370_Ter371insGlu
NP_001338107.1:p.Glu370_Ter371insGlu
NP_001338108.1:p.Glu370_Ter371insGlu
NP_001338108.1:p.Glu370_Ter371insGlu
NP_001338109.1:p.Glu370_Ter371insGlu
NP_001338109.1:p.Glu370_Ter371insGlu
NP_001338110.1:p.Glu370_Ter371insGlu
NP_001338110.1:p.Glu370_Ter371insGlu
NP_001338111.1:p.Glu370_Ter371insGlu
NP_001338111.1:p.Glu370_Ter371insGlu
NP_001338112.1:p.Glu370_Ter371insGlu
NP_001338112.1:p.Glu370_Ter371insGlu
NP_001338113.1:p.Glu370_Ter371insGlu
NP_001338113.1:p.Glu370_Ter371insGlu
NP_001338114.1:p.Glu370_Ter371insGlu
NP_001338114.1:p.Glu370_Ter371insGlu
NP_001338115.1:p.Glu370_Ter371insGlu
NP_001338115.1:p.Glu370_Ter371insGlu
NP_001338116.1:p.Glu370_Ter371insGlu
NP_001338116.1:p.Glu370_Ter371insGlu
NP_001338117.1:p.Glu370_Ter371insGlu
NP_001338117.1:p.Glu370_Ter371insGlu
NP_001338118.1:p.Glu370_Ter371insGlu
NP_001338118.1:p.Glu370_Ter371insGlu
NP_001338119.1:p.Glu370_Ter371insGlu
NP_001338119.1:p.Glu370_Ter371insGlu
NP_001338120.1:p.Glu370_Ter371insGlu
NP_001338121.1:p.Glu370_Ter371insGlu
NP_001338122.1:p.Glu370_Ter371insGlu
NP_001338123.1:p.Glu323_Ter324insGlu
NP_001338123.1:p.Glu323_Ter324insGlu
NP_001338124.1:p.Glu323_Ter324insGlu
NP_001338124.1:p.Glu323_Ter324insGlu
NP_001338125.1:p.Glu323_Ter324insGlu
NP_001338125.1:p.Glu323_Ter324insGlu
NP_001338126.1:p.Glu370_Ter371insGlu
NP_001338126.1:p.Glu370_Ter371insGlu
NP_036361.1:p.Glu561_Ter562insGlu
NP_036361.1:p.Glu561_Ter562insGlu
NC_000010.10:g.104849431_104849432insTTC
NC_000010.10:g.104849432TTC[3]
NM_001134373.2:c.1678_1680GAA[3]
NM_001351169.1:c.1678_1680GAA[3]
NM_001351170.1:c.1702_1704GAA[3]
NM_001351171.1:c.1702_1704GAA[3]
NM_001351172.1:c.1702_1704GAA[3]
NM_001351173.1:c.1702_1704GAA[3]
NM_001351175.1:c.1585_1587GAA[3]
NM_001351176.1:c.1105_1107GAA[3]
NM_001351177.1:c.1105_1107GAA[3]
NM_001351178.1:c.1105_1107GAA[3]
NM_001351179.1:c.1105_1107GAA[3]
NM_001351180.1:c.1105_1107GAA[3]
NM_001351181.1:c.1105_1107GAA[3]
NM_001351182.1:c.1105_1107GAA[3]
NM_001351183.1:c.1105_1107GAA[3]
NM_001351184.1:c.1105_1107GAA[3]
NM_001351185.1:c.1105_1107GAA[3]
NM_001351186.1:c.1105_1107GAA[3]
NM_001351187.1:c.1105_1107GAA[3]
NM_001351188.1:c.1105_1107GAA[3]
NM_001351189.1:c.1105_1107GAA[3]
NM_001351190.1:c.1105_1107GAA[3]
NM_001351194.1:c.964_966GAA[3]
NM_001351195.1:c.964_966GAA[3]
NM_001351196.1:c.964_966GAA[3]
NM_001351197.1:c.1105_1107GAA[3]
NM_012229.4:c.1678_1680GAA[3]

Molecular consequence:

NM_017649.5:c.*12495TTC[3] - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_199076.3:c.*12495TTC[3] - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001134373.3:c.1678GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351169.2:c.1678GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351170.2:c.1702GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351171.2:c.1702GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351172.2:c.1702GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351173.2:c.1702GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351174.1:c.1591GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351175.2:c.1585GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351176.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351177.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351178.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351179.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351180.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351181.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351182.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351183.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351184.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351185.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351186.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351187.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351188.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351189.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351190.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351191.1:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351192.1:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351193.1:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351194.2:c.964GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351195.2:c.964GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351196.2:c.964GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001351197.2:c.1105GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_012229.5:c.1678GAA[3] - inframe_insertion - [Sequence Ontology: SO:0001821]

Condition(s)

Name:: Hereditary spastic paraplegia 45
Synonyms:: Spastic paraplegia 45, autosomal recessive; SPASTIC PARAPLEGIA 45
Identifiers:: MONDO: MONDO:0013165; MedGen: C3888209; Orphanet: 320396; OMIM: 613162

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002989095	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 29, 2022)	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

SCV002989095

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 29, 2022)

germline

clinical testing

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

Help

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002989095.2

#	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 disrupts the translational stop signal of the NT5C2 mRNA. It is expected to extend the length of the NT5C2 protein by 1 additional amino acid residues. This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with NT5C2-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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

Last Updated: Sep 29, 2024

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