USH2A A125T - GET-Evidence

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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.

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Curation:
Currentness:

USH2A A125T

(USH2A Ala125Thr)


Short summary

 

Variant evidence
Computational 1

Variant Effect Predictor (Ensembl ):
SIFT=tolerated(0.11);
PolyPhen=benign(0);
Condel=deleterious(0.890)
Mutation Tasting Prediction: Polymorphism p value: 0.999999; protein features (might be) affected (Detail: aa 32-5042 TOPO_DOMAIN Extracellular (potential) gets lost)
GVGD: GV 353.86; GD 0.00; Class C0
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

  • T @ chr1:216595306: 71.9% (7736/10758) in EVS
  • T @ chr1:214661928: 72.7% (93/128) in GET-Evidence
  • Frequency shown in summary reports: 71.9% (7736/10758)

Publications
 

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
het T @ chr1:216595306

 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
het T @ chr1:216595306

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het T @ chr1:216595306

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
hom T @ chr1:216595306

 

hu0E64A1 - CGI sample GS01173-DNA_B02 from PGP sample 94378523
hom T @ chr1:216595306

 

hu232307 - PGP14 (hu232307) build 36, substitution variants, hu232307 build 36 substitution variants
hom T @ chr1:214661929

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
het T @ chr1:216595306

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
hom T @ chr1:216595306

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
het T @ chr1:216595306

 

hu3215A7 - PGP12 (hu3215A7) build 36, substitution variants, hu3215A7 build 36 substitution variants
het T @ chr1:214661929

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
het T @ chr1:216595306

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
het T @ chr1:216595306

 

hu3A8D13 - PGP13 (hu3A8D13) build 37, from CGI var (software ver 1.11.0.16), CGI sample GS000003289
het T @ chr1:216595306

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het T @ chr1:216595306

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
hom T @ chr1:216595306

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het T @ chr1:216595306

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het T @ chr1:216595306

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
het T @ chr1:216595306

 

hu4CA5B9 - CGI sample GS01669-DNA_B03 from PGP sample 14427241
het T @ chr1:216595306

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
hom T @ chr1:216595306

 

hu728FFF - PGP11 (hu728FFF) build 36, substitution variants, hu728FFF build 36 substitution variants
hom T @ chr1:214661929

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het T @ chr1:216595306

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
hom T @ chr1:216595306

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het T @ chr1:216595306

 

hu92FD55 - CGI sample GS01669-DNA_A04 from PGP sample 08188426
hom T @ chr1:216595306

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
hom T @ chr1:216595306

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
hom T @ chr1:216595306

 

huA90CE6 - PGP16 (huA90CE6) build 37, from CGI var (software ver 2.0.2.11), CGI sample GS000006909
hom T @ chr1:216595306

 

huAE4A11 - CGI sample GS01669-DNA_F02 from PGP sample 40767107
het T @ chr1:216595306

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
hom T @ chr1:216595306

 

huB1FD55 - CGI sample GS01173-DNA_B07 from PGP sample 61499538
het T @ chr1:216595306

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
hom T @ chr1:216595306

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het T @ chr1:216595306

 

huCA017E - CGI sample GS01175-DNA_B01 from PGP sample 86206034
hom T @ chr1:216595306

 

huD37D14 - CGI sample GS01175-DNA_A04 from PGP sample 13272228
hom T @ chr1:216595306

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
hom T @ chr1:216595306

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
hom T @ chr1:216595306

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
hom T @ chr1:216595306

 

huFFAD87 - CGI sample GS01669-DNA_H05 from PGP sample 10971581
hom T @ chr1:216595306

 

GS06985 - var-GS06985-1100-36-ASM
hom T @ chr1:214661929

 

GS07357 - var-GS07357-1100-36-ASM
het T @ chr1:214661929

 

GS10851 - var-GS10851-1100-36-ASM
hom T @ chr1:214661929

 

GS18501 - var-GS18501-1100-36-ASM
hom T @ chr1:214661929

 

GS18502 - var-GS18502-1100-36-ASM
hom T @ chr1:214661929

 

GS18504 - var-GS18504-1100-36-ASM
hom T @ chr1:214661929

 

GS18505 - var-GS18505-1100-36-ASM
het T @ chr1:214661929

 

GS18508 - var-GS18508-1100-36-ASM
het T @ chr1:214661929

 

GS18517 - var-GS18517-1100-36-ASM
het T @ chr1:214661929

 

GS18526 - var-GS18526-1100-36-ASM
het T @ chr1:214661929

 

GS18537 - var-GS18537-1100-36-ASM
het T @ chr1:214661929

 

GS18555 - var-GS18555-1100-36-ASM
hom T @ chr1:214661929

 

GS18558 - var-GS18558-1100-36-ASM
hom T @ chr1:214661929

 

GS18940 - var-GS18940-1100-36-ASM
hom T @ chr1:214661929

 

GS18942 - var-GS18942-1100-36-ASM
het T @ chr1:214661929

 

GS18947 - var-GS18947-1100-36-ASM
hom T @ chr1:214661929

 

GS18956 - var-GS18956-1100-36-ASM
het T @ chr1:214661929

 

GS19017 - var-GS19017-1100-36-ASM
het T @ chr1:214661929

 

GS19020 - var-GS19020-1100-36-ASM
het T @ chr1:214661929

 

GS19025 - var-GS19025-1100-36-ASM
hom T @ chr1:214661929

 

GS19026 - var-GS19026-1100-36-ASM
hom T @ chr1:214661929

 

GS19129 - var-GS19129-1100-36-ASM
hom T @ chr1:214661929

 

GS19238 - var-GS19238-1100-36-ASM
hom T @ chr1:214661929

 

GS19239 - var-GS19239-1100-36-ASM
hom T @ chr1:214661929

 

GS19240 - var-GS19240-1100-36-ASM
hom T @ chr1:214661929

 

GS19648 - var-GS19648-1100-36-ASM
het T @ chr1:214661929

 

GS19669 - var-GS19669-1100-36-ASM
het T @ chr1:214661929

 

GS19670 - var-GS19670-1100-36-ASM
hom T @ chr1:214661929

 

GS19700 - var-GS19700-1100-36-ASM
hom T @ chr1:214661929

 

GS19701 - var-GS19701-1100-36-ASM
het T @ chr1:214661929

 

GS19703 - var-GS19703-1100-36-ASM
het T @ chr1:214661929

 

GS19704 - var-GS19704-1100-36-ASM
hom T @ chr1:214661929

 

GS19735 - var-GS19735-1100-36-ASM
het T @ chr1:214661929

 

GS19834 - var-GS19834-1100-36-ASM
het T @ chr1:214661929

 

GS20502 - var-GS20502-1100-36-ASM
hom T @ chr1:214661929

 

GS20509 - var-GS20509-1100-36-ASM
hom T @ chr1:214661929

 

GS21767 - var-GS21767-1100-36-ASM
hom T @ chr1:214661929

 

Other external references
 

    dbSNP
  • rs10779261
    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 (benign)
    Web search results (13 hits -- see all)
  • USH2A SNPs - Genomewiki
    Usherin (USH2A), a 71-exon gene located on human chromosome 1q41] ... USH2A, while resembling a shuffle of ubiquitious domains, has potential ...
    genomewiki.ucsc.edu/index.php/USH2A_SNPs
  • Novel USH2A Mutations in Israeli Patients With Retinitis ...
    The analysis revealed 3 USH2A mutations, 2 of which are novel, in 2 ... B, Single nucleotide polymorphisms and USH2A mutations in 3 Israeli families. ...
    archopht.ama-assn.org/cgi/reprint/125/2/219.pdf

Other in silico analyses
 

  • NBLOSUM100 score = 1
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

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