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NM_001351169.2(NT5C2):c.1624del (p.Gln542fs) AND Hereditary spastic paraplegia 45

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 4, 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:
RCV002250160.1

Allele description [Variation Report for NM_001351169.2(NT5C2):c.1624del (p.Gln542fs)]

NM_001351169.2(NT5C2):c.1624del (p.Gln542fs)

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:
Deletion
Cytogenetic location:
10q24.32
Genomic location:
Preferred name:
NM_001351169.2(NT5C2):c.1624del (p.Gln542fs)
HGVS:
  • NC_000010.11:g.103089739del
  • NG_042272.1:g.108573del
  • NM_001134373.3:c.1624del
  • NM_001351169.2:c.1624delMANE SELECT
  • NM_001351170.2:c.1648del
  • NM_001351171.2:c.1648del
  • NM_001351172.2:c.1648del
  • NM_001351173.2:c.1648del
  • NM_001351174.1:c.1537del
  • NM_001351175.2:c.1531del
  • NM_001351176.2:c.1051del
  • NM_001351177.2:c.1051del
  • NM_001351178.2:c.1051del
  • NM_001351179.2:c.1051del
  • NM_001351180.2:c.1051del
  • NM_001351181.2:c.1051del
  • NM_001351182.2:c.1051del
  • NM_001351183.2:c.1051del
  • NM_001351184.2:c.1051del
  • NM_001351185.2:c.1051del
  • NM_001351186.2:c.1051del
  • NM_001351187.2:c.1051del
  • NM_001351188.2:c.1051del
  • NM_001351189.2:c.1051del
  • NM_001351190.2:c.1051del
  • NM_001351191.1:c.1051del
  • NM_001351192.1:c.1051del
  • NM_001351193.1:c.1051del
  • NM_001351194.2:c.910del
  • NM_001351195.2:c.910del
  • NM_001351196.2:c.910del
  • NM_001351197.2:c.1051del
  • NM_012229.5:c.1624del
  • NM_017649.5:c.*12559delMANE SELECT
  • NM_199076.3:c.*12559del
  • NP_001127845.1:p.Gln542fs
  • NP_001338098.1:p.Gln542fs
  • NP_001338099.1:p.Gln550fs
  • NP_001338100.1:p.Gln550fs
  • NP_001338101.1:p.Gln550fs
  • NP_001338102.1:p.Gln550fs
  • NP_001338103.1:p.Gln513fs
  • NP_001338104.1:p.Gln511fs
  • NP_001338105.1:p.Gln351fs
  • NP_001338106.1:p.Gln351fs
  • NP_001338107.1:p.Gln351fs
  • NP_001338108.1:p.Gln351fs
  • NP_001338109.1:p.Gln351fs
  • NP_001338110.1:p.Gln351fs
  • NP_001338111.1:p.Gln351fs
  • NP_001338112.1:p.Gln351fs
  • NP_001338113.1:p.Gln351fs
  • NP_001338114.1:p.Gln351fs
  • NP_001338115.1:p.Gln351fs
  • NP_001338116.1:p.Gln351fs
  • NP_001338117.1:p.Gln351fs
  • NP_001338118.1:p.Gln351fs
  • NP_001338119.1:p.Gln351fs
  • NP_001338120.1:p.Gln351fs
  • NP_001338121.1:p.Gln351fs
  • NP_001338122.1:p.Gln351fs
  • NP_001338123.1:p.Gln304fs
  • NP_001338124.1:p.Gln304fs
  • NP_001338125.1:p.Gln304fs
  • NP_001338126.1:p.Gln351fs
  • NP_036361.1:p.Gln542fs
  • NC_000010.10:g.104849496del
  • NC_000010.11:g.103089734_103089734delG
Protein change:
Q304fs
Links:
dbSNP: rs1385107002
NCBI 1000 Genomes Browser:
rs1385107002
Molecular consequence:
  • NM_017649.5:c.*12559del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_199076.3:c.*12559del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001134373.3:c.1624del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351169.2:c.1624del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351170.2:c.1648del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351171.2:c.1648del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351172.2:c.1648del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351173.2:c.1648del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351174.1:c.1537del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351175.2:c.1531del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351176.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351177.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351178.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351179.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351180.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351181.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351182.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351183.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351184.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351185.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351186.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351187.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351188.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351189.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351190.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351191.1:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351192.1:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351193.1:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351194.2:c.910del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351195.2:c.910del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351196.2:c.910del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001351197.2:c.1051del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_012229.5:c.1624del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV002517822Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2019)		Pathogenic
(May 4, 2022) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Mendelics, SCV002517822.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Dec 24, 2023