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NM_001776.6(ENTPD1):c.1174C>T (p.Gln392Ter) AND Hereditary spastic paraplegia 64

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 15, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV004560360.1

Allele description

NM_001776.6(ENTPD1):c.1174C>T (p.Gln392Ter)

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.1174C>T (p.Gln392Ter)
HGVS:
  • NC_000010.11:g.95860568C>T
  • NG_042803.1:g.153790C>T
  • NG_042803.2:g.171384C>T
  • NM_001098175.2:c.1195C>T
  • NM_001164178.1:c.1210C>T
  • NM_001164179.2:c.1051C>T
  • NM_001164181.1:c.850C>T
  • NM_001164182.2:c.760C>T
  • NM_001164183.2:c.760C>T
  • NM_001312654.1:c.850C>T
  • NM_001320916.1:c.1210C>T
  • NM_001776.6:c.1174C>TMANE SELECT
  • NP_001091645.1:p.Gln399Ter
  • NP_001157650.1:p.Gln404Ter
  • NP_001157651.1:p.Gln351Ter
  • NP_001157653.1:p.Gln284Ter
  • NP_001157654.1:p.Gln254Ter
  • NP_001157655.1:p.Gln254Ter
  • NP_001299583.1:p.Gln284Ter
  • NP_001307845.1:p.Gln404Ter
  • NP_001767.3:p.Gln392Ter
  • NC_000010.10:g.97620325C>T
Protein change:
Q254*
Molecular consequence:
  • NM_001098175.2:c.1195C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001164178.1:c.1210C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001164179.2:c.1051C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001164181.1:c.850C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001164182.2:c.760C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001164183.2:c.760C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001312654.1:c.850C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001320916.1:c.1210C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001776.6:c.1174C>T - nonsense - [Sequence Ontology: SO:0001587]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV005043790Dr Sami Ulus Medical Genetics Department, Dr Sami Ulus Training and Research Hospital for Maternity and Children's Health and Diseases
no assertion criteria provided
Pathogenic
(May 15, 2024) 		germlineresearch

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Turkishgermlineyes1not providednot providednot providednot providedresearch

Details of each submission

From Dr Sami Ulus Medical Genetics Department, Dr Sami Ulus Training and Research Hospital for Maternity and Children's Health and Diseases, SCV005043790.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Turkish1not providednot providedresearchnot provided

Description

The homozygous Gln392Ter variant identified in ENTPD1 has not been reported in gnomAD v.4.1.0 (807,162 samples). As this variant is a nonsense variant, it is predicted to undergo nonsense mediated decay and is expected to lead to loss of function of the protein, but no experimental studies have been performed to support this prediction. In conclusion, the Gln392Ter variant meets the criteria to be classified as pathogenic based on segregation studies and absence in the healthy population.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Jun 17, 2024