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NM_025137.4(SPG11):c.7212T>C (p.Tyr2404=) AND Inborn genetic diseases

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jul 11, 2019
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:
RCV002369692.9

Allele description [Variation Report for NM_025137.4(SPG11):c.7212T>C (p.Tyr2404=)]

NM_025137.4(SPG11):c.7212T>C (p.Tyr2404=)

Gene:
SPG11:SPG11 vesicle trafficking associated, spatacsin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q21.1
Genomic location:
Preferred name:
NM_025137.4(SPG11):c.7212T>C (p.Tyr2404=)
HGVS:
  • NC_000015.10:g.44563241A>G
  • NG_008885.1:g.105438T>C
  • NM_001160227.2:c.6873T>C
  • NM_025137.4:c.7212T>CMANE SELECT
  • NP_001153699.1:p.Tyr2291=
  • NP_079413.3:p.Tyr2404=
  • NC_000015.9:g.44855439A>G
  • NM_025137.3:c.7212T>C
Links:
dbSNP: rs1288255586
NCBI 1000 Genomes Browser:
rs1288255586
Molecular consequence:
  • NM_001160227.2:c.6873T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_025137.4:c.7212T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:
Inborn genetic diseases
Identifiers:
MeSH: D030342; MedGen: C0950123

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002668743Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Jul 11, 2019) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV002668743.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024