USH2A I1665T - 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:

USH2A I1665T

(USH2A Ile1665Thr)


Short summary

 

Variant evidence
Computational -

Variant Effect Predictor (Ensembl ):
SIFT=tolerated(0.31);
PolyPhen=benign(0.029);
Condel=neutral(0.322)
Mutation Tasting Prediction: Disease causing, p value: 0.596777; protein features (might be) affected (Detail: aa 32-5042 TOPO_DOMAIN Extracellular (potential) gets lost)
SIFT: Affect protein function 0.01
GVGD: GV 28.68; GD 69.84; Class C25
Multi-alignment of O75445.3 Usher syndrome 2A (autosomal recessive, mild) [Homo sapiens] with: XP_514197.2 [Pan troglodytes] XP_514197.2 [Pan troglodytes] XP_002760562.1 [Callithrix jacchus] XP_001915680.1 [Equus caballus] NP_001178354.1 [Bos taurus] XP_545710.2 [Canis familiaris] XP_002693994.1 [Bos taurus] XP_002924255.1 [Ailuropoda melanoleuca] XP_001375119.1 [Monodelphis domestica] EFB20486.1 [Ailuropoda melanoleuca] NP_067383.3 [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

  • G @ chr1:216258213: 11.2% (1200/10754) in EVS
  • G @ chr1:214324835: 4.7% (6/128) in GET-Evidence
  • Frequency shown in summary reports: 11.2% (1200/10754)

Publications
 

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
het G @ chr1:216258213

 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
het G @ chr1:216258213

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
het G @ chr1:216258213

 

 

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het G @ chr1:216258213

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
het G @ chr1:216258213

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
het G @ chr1:216258213

 

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het G @ chr1:216258213

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het G @ chr1:216258213

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
hom G @ chr1:216258213

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het G @ chr1:216258213

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het G @ chr1:216258213

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
het G @ chr1:216258213

 

GS07357 - var-GS07357-1100-36-ASM
het G @ chr1:214324836

 

GS18956 - var-GS18956-1100-36-ASM
het G @ chr1:214324836

 

GS19701 - var-GS19701-1100-36-ASM
het G @ chr1:214324836

 

NA12878

 

Other external references
 

    dbSNP
  • rs56222536
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the USH2A gene
    Retinitis Pigmentosa, Autosomal Recessive
    Usher Syndrome Type 2
    USH2A-Related Retinitis Pigmentosa
    Usher Syndrome Type 2A
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/USH2A
    PolyPhen-2
  • Score: 0.3 (possibly damaging)

Other in silico analyses
 

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

Edit history
 

Gene search

"GENE" or "GENE A123C":

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