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Adult onset hereditary spastic paraplegia v2.9 SPTAN1 Achchuthan Shanmugasundram changed review comment from: Comment on classification: This gene should be rated Green as there are several unrelated cases (many more than three cases identified with different variants) from multiple ethnicities reported with spastic paraplegia and supported by functional studies.

OMIM reports Developmental and epileptic encephalopathy 5 (OMIM #613477) as a phenotype for SPTAN1 variants. Spastic quadriplegia is one of the clinical manifestations that has been reported as part of this phenotype.

Two of three patients identified with SPTAN1 variants in PMID:20493457 were reported with spastic quadriplegia, while it has also been reported in one year old male from PMID:22656320 and two patients from PMID:18065176. Out of 22 patients from 14 families identified with SPTAN1 variants in PMID:35150594, fifteen patients from seven families displaying p.Arg19Trp variant were reported with hereditary spastic paraplegia with age of onset ranging from congenital to adolescence, while three other patients displaying other variants (p.Arg1624Cys, p.Arg1098Cys & p.Gln2205Pro) displayed different extremes of spastic ataxia spectrum.

In PMID:36331550, authors carried out SPTAN1 gene enrichment analysis in the rare disease component of the 100,000 Genomes Project and screened 100,000 Genomes Project, DECIPHER database, and GeneMatcher to identify individuals with SPTAN1 variants. Statistically significant enrichment of rare probably damaging SPTAN1 variants were identified in families with hereditary ataxia (HA) or spastic paraplegia (HSP). Out of 31 individuals identified with SPTAN1 variants, five (three families) were presented with complex HA/HSP, two were presented with complex HSP and one with pure HSP.
Sources: Literature; to: Comment on classification: This gene should be rated Green as there are several unrelated cases (many more than three cases identified with different variants) reported with spastic paraplegia and supported by functional studies. Both autosomal dominant and autosomal recessive variants of this gene are implicated in spastic paraplegia and at least three cases are reported for both disorders.

Autosomal dominant disorder:

OMIM reports Developmental and epileptic encephalopathy 5 (OMIM #613477) as a phenotype for SPTAN1 variants. Spastic quadriplegia is one of the clinical manifestations that has been reported as part of this phenotype.

Two of three patients identified with SPTAN1 variants in PMID:20493457 were reported with spastic quadriplegia, while it has also been reported in one year old male from PMID:22656320 and two patients from PMID:18065176. Out of 22 patients from 14 families identified with SPTAN1 variants in PMID:35150594, fifteen patients from seven families displaying p.Arg19Trp variant were reported with hereditary spastic paraplegia with age of onset ranging from congenital to adolescence, while three other patients displaying other variants (p.Arg1624Cys, p.Arg1098Cys & p.Gln2205Pro) displayed different extremes of spastic ataxia spectrum.

In PMID:36331550, authors carried out SPTAN1 gene enrichment analysis in the rare disease component of the 100,000 Genomes Project and screened 100,000 Genomes Project, DECIPHER database, and GeneMatcher to identify individuals with SPTAN1 variants. Statistically significant enrichment of rare probably damaging SPTAN1 variants were identified in families with hereditary ataxia (HA) or spastic paraplegia (HSP). Out of 31 individuals identified with SPTAN1 variants, five (three families) were presented with complex HA/HSP, two were presented with complex HSP and one with pure HSP.

Autosomal recessive disorder:

PMID:31515523 reported two cases of juvenile/ adult-onset spastic paraplegia caused by compound heterozygous variants (p.Ala858Ser/ p.Ala1428Gly & p.Ala858Ser/ Met2330Ile). PMID:34526651 reported a female patient with juvenile/ adult-onset spastic paraplegia and was identified with homozygous missense variant p.Ile1388Val.
Sources: Literature
Adult onset hereditary spastic paraplegia v2.8 SPTAN1 Achchuthan Shanmugasundram gene: SPTAN1 was added
gene: SPTAN1 was added to Hereditary spastic paraplegia - adult onset. Sources: Literature
Mode of inheritance for gene: SPTAN1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: SPTAN1 were set to 18065176; 20493457; 22656320; 35150594; 36331550
Phenotypes for gene: SPTAN1 were set to Developmental and epileptic encephalopathy 5, OMIM:613477; Cerebellar ataxia, MONDO:0000437; Hereditary spastic paraplegia, MONDO:0019064
Review for gene: SPTAN1 was set to GREEN
Added comment: Comment on classification: This gene should be rated Green as there are several unrelated cases (many more than three cases identified with different variants) from multiple ethnicities reported with spastic paraplegia and supported by functional studies.

OMIM reports Developmental and epileptic encephalopathy 5 (OMIM #613477) as a phenotype for SPTAN1 variants. Spastic quadriplegia is one of the clinical manifestations that has been reported as part of this phenotype.

Two of three patients identified with SPTAN1 variants in PMID:20493457 were reported with spastic quadriplegia, while it has also been reported in one year old male from PMID:22656320 and two patients from PMID:18065176. Out of 22 patients from 14 families identified with SPTAN1 variants in PMID:35150594, fifteen patients from seven families displaying p.Arg19Trp variant were reported with hereditary spastic paraplegia with age of onset ranging from congenital to adolescence, while three other patients displaying other variants (p.Arg1624Cys, p.Arg1098Cys & p.Gln2205Pro) displayed different extremes of spastic ataxia spectrum.

In PMID:36331550, authors carried out SPTAN1 gene enrichment analysis in the rare disease component of the 100,000 Genomes Project and screened 100,000 Genomes Project, DECIPHER database, and GeneMatcher to identify individuals with SPTAN1 variants. Statistically significant enrichment of rare probably damaging SPTAN1 variants were identified in families with hereditary ataxia (HA) or spastic paraplegia (HSP). Out of 31 individuals identified with SPTAN1 variants, five (three families) were presented with complex HA/HSP, two were presented with complex HSP and one with pure HSP.
Sources: Literature
Adult onset hereditary spastic paraplegia v1.95 ARG1 Ivone Leong Tag Q3_21_phenotype was removed from gene: ARG1.
Adult onset hereditary spastic paraplegia v1.95 ARG1 Sarah Leigh commented on gene: ARG1
Adult onset hereditary spastic paraplegia v1.94 ARG1 Ivone Leong Source Expert Review Amber was added to ARG1.
Rating Changed from Green List (high evidence) to Amber List (moderate evidence)
Adult onset hereditary spastic paraplegia v1.33 ARG1 Arina Puzriakova Tag Q3_21_phenotype tag was added to gene: ARG1.
Adult onset hereditary spastic paraplegia v1.33 ARG1 Arina Puzriakova commented on gene: ARG1
Adult onset hereditary spastic paraplegia v1.7 ARG1 Zornitza Stark reviewed gene: ARG1: Rating: RED; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Adult onset hereditary spastic paraplegia v0.148 ARG1 Louise Daugherty commented on gene: ARG1: Green gene with Amber GLH rating, Gene discussed in view of discrepant rating(s) from GLH(s). Green rating agreed at the GMS Neurology Specialist Test Group Webex on 17th May 2019.
Adult onset hereditary spastic paraplegia v0.146 ARG1 Louise Daugherty Deleted their comment
Adult onset hereditary spastic paraplegia v0.67 ARG1 Louise Daugherty Publications for gene: ARG1 were set to
Adult onset hereditary spastic paraplegia v0.54 ARG1 Louise Daugherty Source Yorkshire and North East GLH was added to ARG1.
Adult onset hereditary spastic paraplegia v0.53 ARG1 Louise Daugherty commented on gene: ARG1: Review and rating submitted byJames Polke (Neurogenetics Laboratory,Institute of Neurology, London), unless specified in the review comment, on behalf of London North GLH for GMS Neurology specialist test group.
Adult onset hereditary spastic paraplegia v0.52 ARG1 Nick Beauchamp reviewed gene: ARG1: Rating: AMBER; Mode of pathogenicity: None; Publications: 2365823, 1463019, 23859858; Phenotypes: ; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Adult onset hereditary spastic paraplegia v0.6 ARG1 Louise Daugherty reviewed gene: ARG1: Rating: AMBER; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance:
Adult onset hereditary spastic paraplegia v0.5 ARG1 James Polke reviewed gene: ARG1: Rating: GREEN; Mode of pathogenicity: ; Publications: ; Phenotypes: Argininaemia, 207800, Progressive spastic tetraplegia; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal
Adult onset hereditary spastic paraplegia v0.4 ARG1 Louise Daugherty Source Expert Review Green was added to ARG1.
Mode of inheritance for gene ARG1 was changed from to BIALLELIC, autosomal or pseudoautosomal
Added phenotypes Progressive spastic tetraplegia; Argininaemia, 207800 for gene: ARG1
Rating Changed from Red List (low evidence) to Green List (high evidence)
Adult onset hereditary spastic paraplegia v0.3 ARG1 Louise Daugherty Source NHS GMS was added to ARG1.
Adult onset hereditary spastic paraplegia v0.2 ARG1 Louise Daugherty gene: ARG1 was added
gene: ARG1 was added to Hereditary spastic paraplegia - adult onset. Sources: London North GLH
Mode of inheritance for gene: ARG1 was set to