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NM_015915.5(ATL1):c.1217AGA[1] (p.Lys407del) AND Hereditary spastic paraplegia 3A

Germline classification:
Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:
Nov 27, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000995703.7

Allele description

NM_015915.5(ATL1):c.1217AGA[1] (p.Lys407del)

Gene:
ATL1:atlastin GTPase 1 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
14q22.1
Genomic location:
Preferred name:
NM_015915.5(ATL1):c.1217AGA[1] (p.Lys407del)
HGVS:
  • NC_000014.9:g.50628128AGA[1]
  • NC_000014.9:g.50628128_50628130AGA[1]
  • NG_009028.1:g.100047AGA[1]
  • NM_001127713.1:c.1217AGA[1]
  • NM_015915.5:c.1217AGA[1]MANE SELECT
  • NM_181598.4:c.1217AGA[1]
  • NP_001121185.1:p.Lys407del
  • NP_056999.2:p.Lys407del
  • NP_853629.2:p.Lys407del
  • LRG_360t1:c.1220_1222del
  • LRG_360t2:c.1217AGA[1]
  • LRG_360:g.100047AGA[1]
  • LRG_360p2:p.Lys407del
  • NC_000014.8:g.51094844_51094846del
  • NC_000014.8:g.51094846AGA[1]
  • NM_015915.4:c.1215_1217delGAA
  • NM_015915.4:c.1220_1222del
Protein change:
K407del
Links:
dbSNP: rs1595625099
NCBI 1000 Genomes Browser:
rs1595625099
Molecular consequence:
  • NM_001127713.1:c.1217AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_015915.5:c.1217AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_181598.4:c.1217AGA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
Observations:
1

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
SCV001150017Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München
criteria provided, single submitter

(Classification criteria August 2017)		Likely pathogenic
(Jun 21, 2018) 		de novoclinical testing

Citation Link,

SCV003442883Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 27, 2023) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not providednot provided1not providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Clinical and genetic study of hereditary spastic paraplegia in Canada.

Chrestian N, Dupré N, Gan-Or Z, Szuto A, Chen S, Venkitachalam A, Brisson JD, Warman-Chardon J, Ahmed S, Ashtiani S, MacDonald H, Mohsin N, Mourabit-Amari K, Provencher P, Boycott KM, Stavropoulos DJ, Dion PA, Ray PN, Suchowersky O, Rouleau GA, Yoon G.

Neurol Genet. 2017 Feb;3(1):e122.

PubMed [citation]
PMID:
27957547
PMCID:
PMC5141523

Monogenic variants in dystonia: an exome-wide sequencing study.

Zech M, Jech R, Boesch S, Škorvánek M, Weber S, Wagner M, Zhao C, Jochim A, Necpál J, Dincer Y, Vill K, Distelmaier F, Stoklosa M, Krenn M, Grunwald S, Bock-Bierbaum T, Fečíková A, Havránková P, Roth J, Příhodová I, Adamovičová M, Ulmanová O, et al.

Lancet Neurol. 2020 Nov;19(11):908-918. doi: 10.1016/S1474-4422(20)30312-4.

PubMed [citation]
PMID:
33098801
PMCID:
PMC8246240
See all PubMed Citations (4)

Details of each submission

From Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München, SCV001150017.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyes1bloodnot provided1not providednot providednot provided

From Invitae, SCV003442883.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This variant, c.1220_1222del, results in the deletion of 1 amino acid(s) of the ATL1 protein (p.Lys407del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with autosomal dominant hereditary spastic paraplegia and/or dystonia (PMID: 27957547, 33098801, 35925862; Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 807547). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Jun 23, 2024