ALMS1 S2111R - 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:

ALMS1 S2111R

(ALMS1 Ser2111Arg)


Short summary

 

Variant evidence
Computational 2

PolyPhen2: Benign, score 0.000
SIFT: Tolerated 0.8
GVGD: GV 124.29; GD 0.00; Class C0
Variant Effect Predictor (Ensembl):
SIFT=tolerated(1);
PolyPhen=benign(0);
Condel=not_computable_was(-1)
Mutation Tasting Prediction: Polymorphism, P value: 0.999955; protein features (might be) affected (aa 538-2199 REGION 34 X 47 AA approximate tandem repeat gets lost; aa 2105-2151 REPEAT 33 gets lost)

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

  • A @ chr2:73679990: 39.0% (3745/9612) in EVS
  • A @ chr2:73533497: 43.8% (56/128) in GET-Evidence
  • Frequency shown in summary reports: 39.0% (3745/9612)

Publications
 

Genomes
 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
het A @ chr2:73679990

 

 

 

 

 

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het A @ chr2:73679990

 

 

 

 

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
hom A @ chr2:73679990

 

 

 

GS06985 - var-GS06985-1100-36-ASM
het A @ chr2:73533498

 

GS06994 - var-GS06994-1100-36-ASM
het A @ chr2:73533498

 

GS10851 - var-GS10851-1100-36-ASM
het A @ chr2:73533498

 

GS18501 - var-GS18501-1100-36-ASM
hom A @ chr2:73533498

 

GS18502 - var-GS18502-1100-36-ASM
hom A @ chr2:73533498

 

GS18504 - var-GS18504-1100-36-ASM
hom A @ chr2:73533498

 

GS18505 - var-GS18505-1100-36-ASM
hom A @ chr2:73533498

 

GS18508 - var-GS18508-1100-36-ASM
hom A @ chr2:73533498

 

GS18517 - var-GS18517-1100-36-ASM
hom A @ chr2:73533498

 

GS19017 - var-GS19017-1100-36-ASM
hom A @ chr2:73533498

 

GS19020 - var-GS19020-1100-36-ASM
hom A @ chr2:73533498

 

GS19025 - var-GS19025-1100-36-ASM
hom A @ chr2:73533498

 

GS19026 - var-GS19026-1100-36-ASM
hom A @ chr2:73533498

 

GS19129 - var-GS19129-1100-36-ASM
het A @ chr2:73533498

 

GS19238 - var-GS19238-1100-36-ASM
hom A @ chr2:73533498

 

GS19239 - var-GS19239-1100-36-ASM
hom A @ chr2:73533498

 

GS19240 - var-GS19240-1100-36-ASM
hom A @ chr2:73533498

 

GS19669 - var-GS19669-1100-36-ASM
het A @ chr2:73533498

 

GS19700 - var-GS19700-1100-36-ASM
hom A @ chr2:73533498

 

GS19701 - var-GS19701-1100-36-ASM
het A @ chr2:73533498

 

GS19703 - var-GS19703-1100-36-ASM
hom A @ chr2:73533498

 

GS19704 - var-GS19704-1100-36-ASM
hom A @ chr2:73533498

 

GS19735 - var-GS19735-1100-36-ASM
hom A @ chr2:73533498

 

GS19834 - var-GS19834-1100-36-ASM
hom A @ chr2:73533498

 

GS20509 - var-GS20509-1100-36-ASM
het A @ chr2:73533498

 

GS21767 - var-GS21767-1100-36-ASM
het A @ chr2:73533498

 

Other external references
 

    dbSNP
  • rs6724782
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    Web search results (7 hits -- see all)
  • SNPs Identified in ALMS1
    S2111R. T/A. WIPGA_03_515. 6860. chr2:73654944. Mis-sense. view. D2250G. A/G. WIPGA_03_517. 6962 ... and Genotyping > Candidate Gene List > ALMS1 Main Page > SNPs Identified in ALMS1 ...
    cardiogenomics.med.harvard.edu/.../ALMS1_validated_SNPs.html
  • Type I- 95%
    ... MYCBPAP Q8TBZ2 S910R 910 VAR_035005 IKK (0.685) Polymorphism (dbSNP: ... 603) Polymorphism (dbSNP:rs8190315) ALMS1 Q8TCU4 S2111R 2111 VAR_025434 PKC (0.825) Polymorphism (dbSNP: ...
    www.nih.go.kr/phosphovariant/html/family_whole/TypeI-_95.txt
  • Type I- 97%
    ... 8047138 NUP93 Q8N1F7 S509R 509 VAR_028160 CAMKL (0.700) Polymorphism (dbSNP:rs17853288) ... 898) Polymorphism (dbSNP:rs8190315) ALMS1 Q8TCU4 S2111R 2111 VAR_025434 PKC (0.825) ...
    www.nih.go.kr/phosphovariant/html/family_whole/TypeI-_97.txt

Other in silico analyses
 

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

Edit history
 

Gene search

"GENE" or "GENE A123C":

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