SETX S2612G - GET-Evidence

Note: This variant has not been sufficiently evaluated by a GET-Evidence editor.

To be considered sufficiently evaluated a variant must have both "variant evidence" and "clinical importance" scores filled in.

Please help improve GET-Evidence by evaluating evidence for this variant!

Curation:
Currentness:

SETX S2612G

(SETX Ser2612Gly)


Short summary

 

Variant evidence
Computational 3

Variant Effect Predictor (Ensembl ):
SIFT=tolerated(0.38);
PolyPhen=benign(0);
Condel=deleterious(0.614)
Mutation Tasting Prediction: Polymorphism p value: 0.999735; no protein features affected.
GVGD: GV 103.39; GD 0.00; Class C0
Multi-alignment of Q7Z333.4 probable helicase senataxin [Homo sapiens] with: XP_520331.2 [Pan troglodytes] XP_002820362.1 [Pongo abelii] XP_002799993.1 [Macaca mulatta] XP_002743464.1 [Callithrix jacchus] XP_002924403.1 [Ailuropoda melanoleuca] XP_001498724.2 [Equus caballus] XP_537811.2 [Canis familiaris] XP_859643.1 [Canis familiaris] NP_932150.2 [Mus musculus] DAA01946.1 [Mus musculus]

Functional -
Case/Control -
Familial -
 
Clinical importance
Severity -
Treatability -
Penetrance -
 

Impact

Insufficiently evaluated not reviewed

(The "insufficiently evaluated" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

unknown

Summary of published research, and additional commentary

 

Allele frequency

  • C @ chr9:135139826: 7.5% (811/10758) in EVS
  • C @ chr9:134129646: 13.5% (17/126) in GET-Evidence
  • Frequency shown in summary reports: 7.5% (811/10758)

Publications
 

Genomes
 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
het C @ chr9:135139826

 

 

 

 

hu92FD55 - CGI sample GS01669-DNA_A04 from PGP sample 08188426
het C @ chr9:135139826

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
hom C @ chr9:135139826

 

GS18502 - var-GS18502-1100-36-ASM
het C @ chr9:134129647

 

GS18508 - var-GS18508-1100-36-ASM
het C @ chr9:134129647

 

GS18517 - var-GS18517-1100-36-ASM
het C @ chr9:134129647

 

GS18555 - var-GS18555-1100-36-ASM
het C @ chr9:134129647

 

GS18942 - var-GS18942-1100-36-ASM
hom C @ chr9:134129647

 

GS18947 - var-GS18947-1100-36-ASM
hom C @ chr9:134129647

 

GS18956 - var-GS18956-1100-36-ASM
hom C @ chr9:134129647

 

GS19026 - var-GS19026-1100-36-ASM
het C @ chr9:134129647

 

GS19703 - var-GS19703-1100-36-ASM
het C @ chr9:134129647

 

GS21767 - var-GS21767-1100-36-ASM
het C @ chr9:134129647

 

Other external references
 

    dbSNP
  • rs3739927
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the SETX gene
    Amyotrophic lateral sclerosis
    Ataxia with Oculomotor Apraxia 2
    SETX-Related Amyotrophic Lateral Sclerosis
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/SETX
    Web search results (7 hits -- see all)
  • Type I- 99%
    ... Reference(s) for phosphorylation site TBX19 O60806 S128F 128 VAR_018387 CMGC (0. ... rs1800520) 9717837 11524731 SETX Q7Z333 S2612G 2612 VAR_018793 CMGC ...
    www.nih.go.kr/phosphovariant/html/group_whole/TypeI-_99.txt
  • Type I- 99%
    ... belgian patient PRB2 P02812 S274P 274 VAR_019695 CK1 (0.632) Con1-, abolishes the glycosylation site at ... PKC (0.962) HeLa cells SETX Q7Z333 S2612G 2612 VAR_018793 CDK (0.983) ...
    www.nih.go.kr/phosphovariant/html/family_whole/TypeI-_99.txt

Other in silico analyses
 

  • NBLOSUM100 score = 2
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

"GENE" or "GENE A123C":

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