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NM_001122955.4(BSCL2):c.455A>G (p.Asn152Ser) AND Hereditary spastic paraplegia 17

Germline classification:
Pathogenic (5 submissions)
Last evaluated:
Apr 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:
RCV000004801.19

Allele description [Variation Report for NM_001122955.4(BSCL2):c.455A>G (p.Asn152Ser)]

NM_001122955.4(BSCL2):c.455A>G (p.Asn152Ser)

Genes:
BSCL2:BSCL2 lipid droplet biogenesis associated, seipin [Gene - OMIM - HGNC]
HNRNPUL2-BSCL2:HNRNPUL2-BSCL2 readthrough (NMD candidate) [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q12.3
Genomic location:
Preferred name:
NM_001122955.4(BSCL2):c.455A>G (p.Asn152Ser)
Other names:
NM_001122955.3(BSCL2):c.455A>G(p.Asn152Ser); NM_001130702.2(BSCL2):c.263A>G(p.Asn88Ser); NM_032667.6(BSCL2):c.263A>G(p.Asn88Ser)
HGVS:
  • NC_000011.10:g.62702499T>C
  • NG_008461.1:g.12076A>G
  • NM_001122955.4:c.455A>GMANE SELECT
  • NM_001130702.2:c.263A>G
  • NM_001386027.1:c.455A>G
  • NM_001386028.1:c.455A>G
  • NM_032667.6:c.263A>G
  • NP_001116427.1:p.Asn152Ser
  • NP_001116427.1:p.Asn152Ser
  • NP_001124174.2:p.Asn88Ser
  • NP_001372956.1:p.Asn152Ser
  • NP_001372957.1:p.Asn152Ser
  • NP_116056.3:p.Asn88Ser
  • LRG_235t1:c.455A>G
  • LRG_235t2:c.263A>G
  • LRG_235:g.12076A>G
  • LRG_235p1:p.Asn152Ser
  • LRG_235p2:p.Asn88Ser
  • NC_000011.9:g.62469971T>C
  • NM_001122955.2:c.455A>G
  • NM_001122955.3:c.455A>G
  • NM_001122955.4:c.455A>G
  • NM_032667.5:c.263A>G
  • NR_037946.1:n.2975A>G
  • Q96G97:p.Asn88Ser
Protein change:
N152S; ASN88SER
Links:
UniProtKB: Q96G97#VAR_022375; OMIM: 606158.0013; dbSNP: rs137852972
NCBI 1000 Genomes Browser:
rs137852972
Molecular consequence:
  • NM_001122955.4:c.455A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001130702.2:c.263A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386027.1:c.455A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001386028.1:c.455A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032667.6:c.263A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_037946.1:n.2975A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
3

Condition(s)

Name:
Hereditary spastic paraplegia 17
Synonyms:
Silver spastic paraplegia syndrome; Spastic paraplegia 17; Spastic paraplegia with amyotrophy of hands and feet; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010043; MedGen: C2931276; Orphanet: 100998; OMIM: 270685

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000024977OMIM
no assertion criteria provided
Pathogenic
(Jun 1, 2013)
germlineliterature only

PubMed (7)
[See all records that cite these PMIDs]

SCV000803451SIB Swiss Institute of Bioinformatics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 31, 2018)
unknowncuration

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

SCV001451143Paris Brain Institute, Inserm - ICM
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicunknownclinical testing

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

SCV002574753GeneReviews
no classification provided
not providedgermlineliterature only

SCV003920745Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL)
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Apr 27, 2023)
germlineresearch

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedliterature only
not providedgermlineyes4not providednot providednot providednot providedresearch
not providedunknownyes3not providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedcuration

Citations

PubMed

Heterozygous missense mutations in BSCL2 are associated with distal hereditary motor neuropathy and Silver syndrome.

Windpassinger C, Auer-Grumbach M, Irobi J, Patel H, Petek E, Hörl G, Malli R, Reed JA, Dierick I, Verpoorten N, Warner TT, Proukakis C, Van den Bergh P, Verellen C, Van Maldergem L, Merlini L, De Jonghe P, Timmerman V, Crosby AH, Wagner K.

Nat Genet. 2004 Mar;36(3):271-6. Epub 2004 Feb 22.

PubMed [citation]
PMID:
14981520

Familial spastic paraplegia with amyotrophy of the hands.

Silver JR.

Ann Hum Genet. 1966 Jul;30(1):69-75. No abstract available.

PubMed [citation]
PMID:
5964029
See all PubMed Citations (12)

Details of each submission

From OMIM, SCV000024977.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (7)

Description

In affected members of 1 English and 4 Austrian families with Silver spastic paraplegia syndrome (SPG17; 270685), Windpassinger et al. (2004) identified heterozygosity for a 263A-G transition (c.263A-G, NM_032667) in the BSCL2 gene, resulting in an asn88-to-ser (N88S) mutation. The English family was the original one reported by Silver (1966). In affected members of 1 Italian, 1 English, and 8 Austrian families with autosomal dominant distal hereditary motor neuronopathy-13 (HMND13; 619112), they identified the N88S mutation.

Auer-Grumbach et al. (2005) reported the phenotypic findings in 90 patients from 1 large Austrian family and 2 unrelated German families with the N88S mutation. There was considerable phenotypic variability, including asymptomatic nonpenetrance (4.4%), subclinical involvement (20%), distal spinal muscular atrophy characterized by prominent hand muscle involvement (31.1%), Silver syndrome (14.5%) with hand muscle involvement and spasticity, a Charcot-Marie-Tooth-like phenotype with distal muscle weakness and wasting of the lower limbs and sensory abnormalities (20%), and spastic paraparesis without hand involvement (10%). Auer-Grumbach et al. (2005) concluded that the N88S mutation causes a motor neuron disease affecting the upper motor neurons, lower motor neurons, or both. Hand muscle involvement was a frequent, although not regular, feature, and sensory involvement was usually not present. Genealogic studies of the Austrian kindred traced the disease to a common parent pair born in 1682.

Van de Warrenburg et al. (2006) reported 2 Dutch families with multiple affected individuals carrying a heterozygous N88S mutation. The phenotype in both families overlapped between Silver syndrome and HMND13. Affected members in both families had foot and lower limb atrophy with slowly progressive hyperreflexia and extensor plantar responses without prominent spasticity. Hand involvement occurred in most patients and was restricted to interosseus muscles.

Brusse et al. (2009) reported 12 members of a large 3-generation Dutch family with phenotypic overlap between Silver syndrome and distal HMND13 who carried a heterozygous N88S mutation. The phenotype was variable, and the distribution of muscle weakness and atrophy included predominantly the feet (in 4), the hands (in 1), or both upper and lower extremities (in 4). Three individuals showed evidence of pyramidal features, including spasticity, hyperreflexia, and extensor plantar responses. Severity of the disease ranged from adolescent patients with disabling muscle weakness to an elderly patient with only mild weakness of the ankle dorsiflexors and bilateral pes cavus. Brusse et al. (2009) noted the extreme phenotypic variability associated with the N88S mutation in their family and in those reported by Auer-Grumbach et al. (2005) and van de Warrenburg et al. (2006), and suggested the presence of other genetic or environmental factors. In their family, Brusse et al. (2009) used genomewide linkage analysis to identify a candidate disease modifier on chromosome 16p13.3-p13.12 between SNPs rs6500882 and rs7192086 that was shared by all 12 affected individuals (maximum lod score of 3.28). One family member without the N88S mutation but with the chromosome 16p haplotype showed mild electrophysiologic abnormalities. Brusse et al. (2009) postulated that a locus on chromosome 16p may contain a disease modifier in their family.

Chaudhry et al. (2013) identified a heterozygous N88S mutation in a man with SPG17. He had onset of weakness of the hands and feet at around 12 years of age. Examination at age 14 showed distal weakness and wasting with clawed hands and flat feet, extensor plantar responses, mild tremor, and distal sensory impairment. The disorder was slowly progressive, and he remained ambulatory with orthotics at age 36. His affected uncle also carried the mutation, as did his unaffected mother, suggesting incomplete penetrance. The mutation was identified by exome sequencing of the proband. The family was originally reported by Ionasescu et al. (1991) as having an X-linked form of CMT (302802).

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

From SIB Swiss Institute of Bioinformatics, SCV000803451.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (4)

Description

This variant is interpreted as a Pathogenic, for Spastic paraplegia 17, autosomal dominant, in Autosomal Dominant manner. The following ACMG Tag(s) were applied: PS4 => Prevalence in affecteds statistically increased over controls. N88S is the most frequent mutation. According to Ito & Suzuki 2009, 40 patients out of 48 patients from 16 families have N88S. In ExAC: 1 individual with N88S out of 60000 (PMID:18790819). PS3 => Well-established functional studies show a deleterious effect (PMID:17387721) (PMID:21750110).

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

From Paris Brain Institute, Inserm - ICM, SCV001451143.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided3not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot provided3not providednot providednot provided

From GeneReviews, SCV002574753.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature onlynot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), SCV003920745.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided4not providednot providedresearch PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided4not providednot providednot provided

Last Updated: Oct 20, 2024