ATP7B V1140A - 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:

ATP7B V1140A

(ATP7B Val1140Ala)


Short summary

 

Variant evidence
Computational 3

PolyPhen2: Benign, score 0.000
SIFT: Tolerated 1.00
GVGD: GV 109.55; GD 0.00; Class C0
Variant Effect Predictor (Ensembl):
SIFT=tolerated(0.79);
PolyPhen=benign(0);
Condel=neutral(0.250)
Mutation Tasting Prediction: Polymorphism, P value: 0.999999; protein features (might be) affected (aa 995-1322 TOPO-DOM Cytoplasmic (potential) 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

  • G @ chr13:52515354: 58.5% (5762/9848) in EVS
  • G @ chr13:51413354: 56.2% (72/128) in GET-Evidence
  • Frequency shown in summary reports: 58.5% (5762/9848)

Publications
 

Genomes
 

hu011C57 - CGI sample GS01669-DNA_B05 from PGP sample 86486261
het G @ chr13:52515354

 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
hom G @ chr13:52515354

 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
hom G @ chr13:52515354

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
hom G @ chr13:52515354

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
het G @ chr13:52515354

 

hu0E64A1 - CGI sample GS01173-DNA_B02 from PGP sample 94378523
het G @ chr13:52515354

 

hu232307 - PGP14 (hu232307) build 36, substitution variants, hu232307 build 36 substitution variants
hom G @ chr13:51413355

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
hom G @ chr13:52515354

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
hom G @ chr13:52515354

 

hu2DBF2D - CGI sample GS01173-DNA_G02 from PGP sample 67180598
hom G @ chr13:52515354

 

hu3215A7 - PGP12 (hu3215A7) build 36, substitution variants, hu3215A7 build 36 substitution variants
het G @ chr13:51413355

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
het G @ chr13:52515354

 

hu34D5B9 - CGI sample GS01173-DNA_C07 from PGP sample 92161424, hu34D5B9 exome
het G @ chr13:52515354

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
hom G @ chr13:52515354

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
hom G @ chr13:52515354

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het G @ chr13:52515354

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
hom G @ chr13:52515354

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
het G @ chr13:52515354

 

hu604D39 - CGI sample GS00253-DNA_B02_200_37
het G @ chr13:52515354

 

hu6E4515 - PGP15 (hu6E4515) build 37, from CGI var (software ver 1.12.0.47), CGI sample GS000005532
het G @ chr13:52515354

 

hu728FFF - PGP11 (hu728FFF) build 36, substitution variants, hu728FFF build 36 substitution variants
het G @ chr13:51413355

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
hom G @ chr13:52515354

 

hu7A4AD1 - CGI sample GS01669-DNA_C05 from PGP sample 42408046
het G @ chr13:52515354

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het G @ chr13:52515354

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het G @ chr13:52515354

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
hom G @ chr13:52515354

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
hom G @ chr13:52515354

 

huA90CE6 - PGP16 (huA90CE6) build 37, from CGI var (software ver 2.0.2.11), CGI sample GS000006909
hom G @ chr13:52515354

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het G @ chr13:52515354

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
hom G @ chr13:52515354

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
het G @ chr13:52515354

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
hom G @ chr13:52515354

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het G @ chr13:52515354

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het G @ chr13:52515354

 

GS06985 - var-GS06985-1100-36-ASM
het G @ chr13:51413355

 

GS06994 - var-GS06994-1100-36-ASM
het G @ chr13:51413355

 

GS07357 - var-GS07357-1100-36-ASM
het G @ chr13:51413355

 

GS10851 - var-GS10851-1100-36-ASM
het G @ chr13:51413355

 

GS12004 - var-GS12004-1100-36-ASM
het G @ chr13:51413355

 

GS18501 - var-GS18501-1100-36-ASM
hom G @ chr13:51413355

 

GS18502 - var-GS18502-1100-36-ASM
hom G @ chr13:51413355

 

GS18504 - var-GS18504-1100-36-ASM
het G @ chr13:51413355

 

GS18508 - var-GS18508-1100-36-ASM
het G @ chr13:51413355

 

GS18517 - var-GS18517-1100-36-ASM
het G @ chr13:51413355

 

GS18526 - var-GS18526-1100-36-ASM
het G @ chr13:51413355

 

GS18537 - var-GS18537-1100-36-ASM
het G @ chr13:51413355

 

GS18555 - var-GS18555-1100-36-ASM
het G @ chr13:51413355

 

GS18956 - var-GS18956-1100-36-ASM
het G @ chr13:51413355

 

GS19017 - var-GS19017-1100-36-ASM
het G @ chr13:51413355

 

GS19020 - var-GS19020-1100-36-ASM
het G @ chr13:51413355

 

GS19025 - var-GS19025-1100-36-ASM
het G @ chr13:51413355

 

GS19026 - var-GS19026-1100-36-ASM
het G @ chr13:51413355

 

GS19129 - var-GS19129-1100-36-ASM
het G @ chr13:51413355

 

GS19238 - var-GS19238-1100-36-ASM
hom G @ chr13:51413355

 

GS19239 - var-GS19239-1100-36-ASM
hom G @ chr13:51413355

 

GS19240 - var-GS19240-1100-36-ASM
hom G @ chr13:51413355

 

GS19648 - var-GS19648-1100-36-ASM
hom G @ chr13:51413355

 

GS19649 - var-GS19649-1100-36-ASM
het G @ chr13:51413355

 

GS19669 - var-GS19669-1100-36-ASM
het G @ chr13:51413355

 

GS19670 - var-GS19670-1100-36-ASM
het G @ chr13:51413355

 

GS19700 - var-GS19700-1100-36-ASM
hom G @ chr13:51413355

 

GS19701 - var-GS19701-1100-36-ASM
het G @ chr13:51413355

 

GS19735 - var-GS19735-1100-36-ASM
het G @ chr13:51413355

 

GS19834 - var-GS19834-1100-36-ASM
het G @ chr13:51413355

 

GS20502 - var-GS20502-1100-36-ASM
het G @ chr13:51413355

 

GS20509 - var-GS20509-1100-36-ASM
hom G @ chr13:51413355

 

GS21767 - var-GS21767-1100-36-ASM
hom G @ chr13:51413355

 

Other external references
 

    dbSNP
  • rs1801249
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PolyPhen-2
  • Score: 0 (benign)
    Web search results (20 hits -- see all)
  • World J Gastroenterol
    Correlation of ATP7B genotype with phenotype in Chinese patients with ... Some exons of ATP7B gene mutations were analyzed in patients with WD ...
    www.wjgnet.com/1007-9327/10/590.asp
  • [Genotype and phenotype correlation in Chinese patients with ...
    Some exons of ATP7B gene mutation were analyzed in patients with WD by using ... V1106I mutation was 1.7%, G943S, V1140A, and V1216M was 0.86% respectively in this study. ...
    www.ncbi.nlm.nih.gov/pubmed/14761325
  • Correlation of ATP7B genotype with phenotype in Chinese ...
    Correlation of ATP7B genotype with phenotype in Chinese patients with Wilson disease. ... G943D, V1140A, V1106I V1216M and 1384del17), six polymorphisms (IVS4 ...
    www.ncbi.nlm.nih.gov/pubmed/14966923
  • World J Gastroenterol
    Correlation of ATP7B genotype with phenotype in Chinese patients with ... G943D, V1140A, V1106I V1216M and 1384del17), six polymorphisms (IVS4 ...
    www.wjgnet.com/1007-9327/abstract_en.asp?v=10&f=590
  • NH2-terminal signals in ATP7B Cu-ATPase mediate its Cu ...
    NH2-terminal signals in ATP7B Cu-ATPase mediate its Cu-dependent anterograde traffic in ... A406S, V456L, and V1140A, represent single-nucleotide polymorphisms ...
    ajpgi.physiology.org/cgi/content/full/289/5/G904
  • Y. Guo, L. Nyasae, L. T. Braiterman and A. L. Hubbard
    copy to map the itinerary of endogenous and exogenous ATP7B under ... AA changes, A406S, V456L, and V1140A, repre- sent single-nucleotide polymorphisms with ...
    ajpgi.physiology.org/cgi/reprint/289/5/G904.pdf
  • ニュースレター
    日本人における ATP7A 及び ATP7B の遺伝子多型解析. Fukushima-Uesaka, H., et al., pp. 565. 574 ATP7A と ATP7B は,銅のトランスポーターであり, 白金系 ... V1140A, D1279G, D1296N, V1297I であった.現在,追 ...
    www.jssx.org/jpn/newsletter/bn-pdf/24-6.pdf
  • Type III 95%
    ... sample, somatic mutation 12355088 ATP7B P35670 Q1142H 1132 VAR_000766 CAMK ... to coronary artery disease 15496429 ATP7B P35670 V456L 452 VAR_000708 CMGC (0. ...
    www.nih.go.kr/phosphovariant/html/group_whole/TypeIII_95.txt
  • Type II- 97%
    ... PROT ID Variant site Phosphorylation site SWISS-PROT variant ID Removed kinase ... CAMK2 (0.906) RSK (0.866) Polymorphism (dbSNP:rs13447) ATP7B P35670 P992L 991 ...
    nih.go.kr/phosphovariant/html/family_whole/TypeII-_97.txt
  • [Genotype and phenotype correlation in Chinese patients with ...
    OBJECTIVE: To determine distribution and mutation pattern of type P ATP7B gene mutation and to explore genotype and phenotype correlation in patients with Wilson's ...
    www.medscape.com/medline/abstract/14761325

Other in silico analyses
 

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

Edit history
 

Gene search

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