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NM_015915.5(ATL1):c.1193C>A (p.Ser398Tyr) AND Hereditary spastic paraplegia 3A

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Jul 6, 2015
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:
RCV000203941.6

Allele description [Variation Report for NM_015915.5(ATL1):c.1193C>A (p.Ser398Tyr)]

NM_015915.5(ATL1):c.1193C>A (p.Ser398Tyr)

Gene:
ATL1:atlastin GTPase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q22.1
Genomic location:
Preferred name:
NM_015915.5(ATL1):c.1193C>A (p.Ser398Tyr)
HGVS:
  • NC_000014.9:g.50628104C>A
  • NG_009028.1:g.100023C>A
  • NM_001127713.1:c.1193C>A
  • NM_015915.5:c.1193C>AMANE SELECT
  • NM_181598.4:c.1193C>A
  • NP_001121185.1:p.Ser398Tyr
  • NP_056999.2:p.Ser398Tyr
  • NP_056999.2:p.Ser398Tyr
  • NP_853629.2:p.Ser398Tyr
  • LRG_360t1:c.1193C>A
  • LRG_360t2:c.1193C>A
  • LRG_360:g.100023C>A
  • LRG_360p1:p.Ser398Tyr
  • LRG_360p2:p.Ser398Tyr
  • NC_000014.8:g.51094822C>A
  • NM_015915.4:c.1193C>A
Protein change:
S398Y
Links:
dbSNP: rs864622083
NCBI 1000 Genomes Browser:
rs864622083
Molecular consequence:
  • NM_001127713.1:c.1193C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015915.5:c.1193C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_181598.4:c.1193C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary spastic paraplegia 3A (SPG3A)
Synonyms:
SPASTIC PARAPLEGIA 3, AUTOSOMAL DOMINANT; FAMILIAL SPASTIC PARAPLEGIA, AUTOSOMAL DOMINANT, 1; SPG3; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008437; MedGen: C2931355; Orphanet: 100984; OMIM: 182600

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000259291Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Jul 6, 2015) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV004011932Inherited Neuropathy Consortium Ii, University Of Miami
no assertion criteria provided
Uncertain significance
(Jan 6, 2016) 		germlineliterature only

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Hereditary spastic paraplegia and axonal motor neuropathy caused by a novel SPG3A de novo mutation.

Fusco C, Frattini D, Farnetti E, Nicoli D, Casali B, Fiorentino F, Nuccitelli A, Giustina ED.

Brain Dev. 2010 Aug;32(7):592-4. doi: 10.1016/j.braindev.2009.08.003. Epub 2009 Sep 6.

PubMed [citation]
PMID:
19735987

Atlastin1 mutations are frequent in young-onset autosomal dominant spastic paraplegia.

Dürr A, Camuzat A, Colin E, Tallaksen C, Hannequin D, Coutinho P, Fontaine B, Rossi A, Gil R, Rousselle C, Ruberg M, Stevanin G, Brice A.

Arch Neurol. 2004 Dec;61(12):1867-72.

PubMed [citation]
PMID:
15596607
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000259291.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

For these reasons, this variant has been classified as Likely Pathogenic. A different missense substitution at this codon (p.Ser398Phe) is reported to be deleterious (PMID: 19735987). This suggests that the serine residue is important for ATL1 protein function. This variant has been reported in the literature and is not present in population databases. This variant was reported in an individual affected with autosomal dominant hereditary spastic paraplegia, although it is unclear if this variant segregated with disease (PMID: 15596607). This sequence change replaces serine with tyrosine at codon 398 of the ATL1 protein (p.Ser398Tyr). The serine residue is moderately conserved and there is a large physicochemical difference between serine and tyrosine.

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

From Inherited Neuropathy Consortium Ii, University Of Miami, SCV004011932.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024