TEP1 S116P - 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:

TEP1 S116P

(TEP1 Ser116Pro)


Short summary

 

Variant evidence
Computational 2

Variant Effect Predictor (Ensembl ):
SIFT=tolerated(1);
PolyPhen=benign(0);
Condel=not_computable_was(-1)
Mutation Tasting Prediction: Polymorphism p value: 0.999994; protein features (might be) affected (Detail: aa 91-120 REPEAT TEP1 N-terminal 4 gets lost)
GVGD: GV 79.02, GD 0.00, Class C0
Multi-alignment of Q99973.2 telomerase protein component 1 [Homo sapiens] with: XP_002824552.1 [Pongo abelii] XP_002753746.1 [Callithrix jacchus] XP_001137917.2 [Pan troglodytes] XP_001505180.2 [Equus caballus] XP_001927242.1 [Sus scrofa] NP_001193841.1 [Bos taurus] XP_002929560.1 [Ailuropoda melanoleuca] EFB21485.1 [Ailuropoda melanoleuca]

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 @ chr14:20876253: 38.5% (4143/10758) in EVS
  • G @ chr14:19946092: 38.3% (49/128) in GET-Evidence
  • Frequency shown in summary reports: 38.5% (4143/10758)

Publications
 

Genomes
 

hu034DB1 - CGI sample GS00253-DNA_A02_200_37
het G @ chr14:20876253

 

hu04FD18 - CGI sample GS00253-DNA_F01_200_37
hom G @ chr14:20876253

 

 

hu38168C - CGI sample GS01173-DNA_H06 from PGP sample 91708424
het G @ chr14:20876253

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het G @ chr14:20876253

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
het G @ chr14:20876253

 

hu4339C0 - CGI sample GS01175-DNA_H01 from PGP sample 94797469
het G @ chr14:20876253

 

hu43860C - CGI sample GS00253-DNA_A01_200_37
het G @ chr14:20876253

 

 

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
het G @ chr14:20876253

 

hu8229AE - CGI sample GS01173-DNA_A07 from PGP sample 96240009
het G @ chr14:20876253

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
hom G @ chr14:20876253

 

hu92FD55 - CGI sample GS01669-DNA_A04 from PGP sample 08188426
het G @ chr14:20876253

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
het G @ chr14:20876253

 

 

huBEDA0B - CGI sample GS00253-DNA_C01_200_37
hom G @ chr14:20876253

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
het G @ chr14:20876253

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het G @ chr14:20876253

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
het G @ chr14:20876253

 

GS07357 - var-GS07357-1100-36-ASM
het G @ chr14:19946093

 

GS10851 - var-GS10851-1100-36-ASM
het G @ chr14:19946093

 

GS12004 - var-GS12004-1100-36-ASM
het G @ chr14:19946093

 

GS18502 - var-GS18502-1100-36-ASM
het G @ chr14:19946093

 

GS18504 - var-GS18504-1100-36-ASM
het G @ chr14:19946093

 

GS18505 - var-GS18505-1100-36-ASM
het G @ chr14:19946093

 

GS18517 - var-GS18517-1100-36-ASM
hom G @ chr14:19946093

 

GS18526 - var-GS18526-1100-36-ASM
het G @ chr14:19946093

 

GS18537 - var-GS18537-1100-36-ASM
het G @ chr14:19946093

 

GS19017 - var-GS19017-1100-36-ASM
het G @ chr14:19946093

 

GS19020 - var-GS19020-1100-36-ASM
hom G @ chr14:19946093

 

GS19025 - var-GS19025-1100-36-ASM
het G @ chr14:19946093

 

GS19026 - var-GS19026-1100-36-ASM
hom G @ chr14:19946093

 

GS19129 - var-GS19129-1100-36-ASM
hom G @ chr14:19946093

 

GS19238 - var-GS19238-1100-36-ASM
het G @ chr14:19946093

 

GS19239 - var-GS19239-1100-36-ASM
het G @ chr14:19946093

 

GS19649 - var-GS19649-1100-36-ASM
het G @ chr14:19946093

 

GS19669 - var-GS19669-1100-36-ASM
het G @ chr14:19946093

 

GS19700 - var-GS19700-1100-36-ASM
hom G @ chr14:19946093

 

GS19701 - var-GS19701-1100-36-ASM
het G @ chr14:19946093

 

GS19703 - var-GS19703-1100-36-ASM
het G @ chr14:19946093

 

GS19735 - var-GS19735-1100-36-ASM
het G @ chr14:19946093

 

GS20502 - var-GS20502-1100-36-ASM
het G @ chr14:19946093

 

GS20509 - var-GS20509-1100-36-ASM
het G @ chr14:19946093

 

GS21767 - var-GS21767-1100-36-ASM
het G @ chr14:19946093

 

Other external references
 

    dbSNP
  • rs1760897
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    GeneTests
  • GeneTests records for the TEP1 gene
    Bannayan-Riley-Ruvalcaba Syndrome
    Cowden Syndrome
    Macrocephaly/Autism Syndrome
    PTEN Hamartoma Tumor Syndrome (PHTS)
    VACTERL Association with Hydrocephalus
    www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/TEP1
    Web search results (4 hits -- see all)
  • AceView: Gene:TEP1, a comprehensive annotation of human ...
    AceView offers a comprehensive annotation of human, mouse and nematode genes reconstructed by co-alignment and clustering of all publicly available mRNAs and ESTs on ...
    ncbi.nlm.nih.gov/IEB/Research/Acembly/...&a=clones&l=TEP1
  • Type I- 99%
    ... Polymorphism (dbSNP:rs4057750) KCNJ11 Q14654 S116P 116 VAR_031337 CK1 ... 701) SCP 15571623 TEP1 Q99973 S1447T 1447 VAR_018494 CK2 (0.890) Polymorphism ...
    www.nih.go.kr/phosphovariant/html/family_whole/TypeI-_99.txt
  • Type I- 97%
    Gene name SWISS-PROT ID Variant site Phosphorylation site SWISS-PROT variant ID ... rs27230) GAD1 Q99259 S12C 12 VAR_031021 CK1 (0.701) SCP 15571623 TEP1 ...
    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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