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NM_001351169.2(NT5C2):c.1323T>C (p.Phe441=) AND Hereditary spastic paraplegia 45

Germline classification:
Likely benign (1 submission)
Last evaluated:
Feb 24, 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:
RCV002630113.3

Allele description [Variation Report for NM_001351169.2(NT5C2):c.1323T>C (p.Phe441=)]

NM_001351169.2(NT5C2):c.1323T>C (p.Phe441=)

Gene:
NT5C2:5'-nucleotidase, cytosolic II [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q24.32
Genomic location:
Preferred name:
NM_001351169.2(NT5C2):c.1323T>C (p.Phe441=)
HGVS:
  • NC_000010.11:g.103090737A>G
  • NG_031932.2:g.177445A>G
  • NG_042272.1:g.107570T>C
  • NM_001134373.3:c.1323T>C
  • NM_001351169.2:c.1323T>CMANE SELECT
  • NM_001351170.2:c.1347T>C
  • NM_001351171.2:c.1347T>C
  • NM_001351172.2:c.1347T>C
  • NM_001351173.2:c.1347T>C
  • NM_001351174.1:c.1236T>C
  • NM_001351175.2:c.1230T>C
  • NM_001351176.2:c.750T>C
  • NM_001351177.2:c.750T>C
  • NM_001351178.2:c.750T>C
  • NM_001351179.2:c.750T>C
  • NM_001351180.2:c.750T>C
  • NM_001351181.2:c.750T>C
  • NM_001351182.2:c.750T>C
  • NM_001351183.2:c.750T>C
  • NM_001351184.2:c.750T>C
  • NM_001351185.2:c.750T>C
  • NM_001351186.2:c.750T>C
  • NM_001351187.2:c.750T>C
  • NM_001351188.2:c.750T>C
  • NM_001351189.2:c.750T>C
  • NM_001351190.2:c.750T>C
  • NM_001351191.1:c.750T>C
  • NM_001351192.1:c.750T>C
  • NM_001351193.1:c.750T>C
  • NM_001351194.2:c.609T>C
  • NM_001351195.2:c.609T>C
  • NM_001351196.2:c.609T>C
  • NM_001351197.2:c.750T>C
  • NM_012229.5:c.1323T>C
  • NP_001127845.1:p.Phe441=
  • NP_001127845.1:p.Phe441=
  • NP_001338098.1:p.Phe441=
  • NP_001338098.1:p.Phe441=
  • NP_001338099.1:p.Phe449=
  • NP_001338099.1:p.Phe449=
  • NP_001338100.1:p.Phe449=
  • NP_001338100.1:p.Phe449=
  • NP_001338101.1:p.Phe449=
  • NP_001338101.1:p.Phe449=
  • NP_001338102.1:p.Phe449=
  • NP_001338102.1:p.Phe449=
  • NP_001338103.1:p.Phe412=
  • NP_001338104.1:p.Phe410=
  • NP_001338104.1:p.Phe410=
  • NP_001338105.1:p.Phe250=
  • NP_001338105.1:p.Phe250=
  • NP_001338106.1:p.Phe250=
  • NP_001338106.1:p.Phe250=
  • NP_001338107.1:p.Phe250=
  • NP_001338107.1:p.Phe250=
  • NP_001338108.1:p.Phe250=
  • NP_001338108.1:p.Phe250=
  • NP_001338109.1:p.Phe250=
  • NP_001338109.1:p.Phe250=
  • NP_001338110.1:p.Phe250=
  • NP_001338110.1:p.Phe250=
  • NP_001338111.1:p.Phe250=
  • NP_001338111.1:p.Phe250=
  • NP_001338112.1:p.Phe250=
  • NP_001338112.1:p.Phe250=
  • NP_001338113.1:p.Phe250=
  • NP_001338113.1:p.Phe250=
  • NP_001338114.1:p.Phe250=
  • NP_001338114.1:p.Phe250=
  • NP_001338115.1:p.Phe250=
  • NP_001338115.1:p.Phe250=
  • NP_001338116.1:p.Phe250=
  • NP_001338116.1:p.Phe250=
  • NP_001338117.1:p.Phe250=
  • NP_001338117.1:p.Phe250=
  • NP_001338118.1:p.Phe250=
  • NP_001338118.1:p.Phe250=
  • NP_001338119.1:p.Phe250=
  • NP_001338119.1:p.Phe250=
  • NP_001338120.1:p.Phe250=
  • NP_001338121.1:p.Phe250=
  • NP_001338122.1:p.Phe250=
  • NP_001338123.1:p.Phe203=
  • NP_001338123.1:p.Phe203=
  • NP_001338124.1:p.Phe203=
  • NP_001338124.1:p.Phe203=
  • NP_001338125.1:p.Phe203=
  • NP_001338125.1:p.Phe203=
  • NP_001338126.1:p.Phe250=
  • NP_001338126.1:p.Phe250=
  • NP_036361.1:p.Phe441=
  • NP_036361.1:p.Phe441=
  • NC_000010.10:g.104850494A>G
  • NM_001134373.2:c.1323T>C
  • NM_001351169.1:c.1323T>C
  • NM_001351170.1:c.1347T>C
  • NM_001351171.1:c.1347T>C
  • NM_001351172.1:c.1347T>C
  • NM_001351173.1:c.1347T>C
  • NM_001351175.1:c.1230T>C
  • NM_001351176.1:c.750T>C
  • NM_001351177.1:c.750T>C
  • NM_001351178.1:c.750T>C
  • NM_001351179.1:c.750T>C
  • NM_001351180.1:c.750T>C
  • NM_001351181.1:c.750T>C
  • NM_001351182.1:c.750T>C
  • NM_001351183.1:c.750T>C
  • NM_001351184.1:c.750T>C
  • NM_001351185.1:c.750T>C
  • NM_001351186.1:c.750T>C
  • NM_001351187.1:c.750T>C
  • NM_001351188.1:c.750T>C
  • NM_001351189.1:c.750T>C
  • NM_001351190.1:c.750T>C
  • NM_001351194.1:c.609T>C
  • NM_001351195.1:c.609T>C
  • NM_001351196.1:c.609T>C
  • NM_001351197.1:c.750T>C
  • NM_012229.4:c.1323T>C
Molecular consequence:
  • NM_001134373.3:c.1323T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351169.2:c.1323T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351170.2:c.1347T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351171.2:c.1347T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351172.2:c.1347T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351173.2:c.1347T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351174.1:c.1236T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351175.2:c.1230T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351176.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351177.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351178.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351179.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351180.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351181.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351182.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351183.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351184.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351185.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351186.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351187.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351188.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351189.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351190.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351191.1:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351192.1:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351193.1:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351194.2:c.609T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351195.2:c.609T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351196.2:c.609T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001351197.2:c.750T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_012229.5:c.1323T>C - synonymous variant - [Sequence Ontology: SO:0001819]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002955227Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Feb 24, 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002955227.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024