HLA-DQB1 A172T - 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:

HLA-DQB1 A172T

(HLA-DQB1 Ala172Thr)


Short summary

 

Variant evidence
Computational 1

PolyPhen2: Benign, score 0.000
SIFT: Tolerated 0.81
GVGD: GV 58.02; GD 0.00; Class C0
Variant Effect Predictor (Ensembl):
SIFT=tolerated(0.18);
PolyPhen=benign(0);
Condel=deleterious(0.824)
Mutation Tasting Prediction: Polymorphism, P value: 0.995313; protein features (might be) affected (aa 33-230 TOPO_DOM Extracellular (Potential) gets lost; aa 127-220 REGION Beta-2 gets lost; aa 129-233 DOMAIN Ig-like C1-type gets lost; 172-176 STRAND 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

  • T @ chr6:32629891: 32.4% (3472/10726) in EVS
  • AGC,GGT,AGT @ chr6:32737866: 43.6% (34/78) in GET-Evidence
  • Frequency shown in summary reports: 32.4% (3472/10726)

Publications
 

Genomes
 

 

 

 

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
hom AGT @ chr6:32629889

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
hom AGT @ chr6:32629889

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
het AGT @ chr6:32629889

 

 

 

 

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
het AGC @ chr6:32629889

 

hu92FD55 - CGI sample GS01669-DNA_A04 from PGP sample 08188426
het AGT @ chr6:32629889

 

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
het AGC @ chr6:32629889

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het AGC @ chr6:32629889

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het T @ chr6:32629891

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
hom AGT @ chr6:32629889

 

 

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het AGT @ chr6:32629889

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
het AGT @ chr6:32629889

 

GS06994 - var-GS06994-1100-36-ASM
het AGT @ chr6:32737867

 

GS10851 - var-GS10851-1100-36-ASM
hom AGT @ chr6:32737867

 

GS18517 - var-GS18517-1100-36-ASM
het T @ chr6:32737869

 

GS18537 - var-GS18537-1100-36-ASM
het AGT @ chr6:32737867

 

GS19649 - var-GS19649-1100-36-ASM
het T @ chr6:32737869

 

GS19669 - var-GS19669-1100-36-ASM
hom T @ chr6:32737869

 

GS19834 - var-GS19834-1100-36-ASM
het T @ chr6:32737869

 

NA19240

 

Other external references
 

    dbSNP
  • rs1049087
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
  • rs1063323
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    Web search results (0 hits -- see all)

Other in silico analyses
 

  • NBLOSUM100 score = 1
  • GET-Evidence autoscore = 2

Edit history
 

Gene search

"GENE" or "GENE A123C":

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