SALL4 L507R - GET-Evidence

Note: This variant has not been sufficiently evaluated by a GET-Evidence editor.

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Curation:
Currentness:

SALL4 L507R

(SALL4 Leu507Arg)


Short summary

Although the exact function of the SALL4 protein is unknown, mutations in the SALL4 gene have been associated with Okihiro syndrome, acro-renal-ocular syndrome, and IVIC syndrome. Most SALL4-related disorders are autosomal dominant.

Variant evidence
Computational 1

Most SALL4 gene mutations are nonsense mutations.
PolyPhen2: Possibly damaging 0.364
SIFT: Affect protein function 0.00
:GVGD: GV 234.72; GD 91.58; Class C0
Variant Effect Predictor (Ensembl):
SIFT=tolerated(0.39);
PolyPhen=possibly_damaging(0.364);
Condel=neutral(0.383)
Mutation Tasting Prediction: Polymorphism, P value: 0.505717; protein features (might be) affected.

Functional -
Case/Control -
Familial -
 
Clinical importance
Severity 3

Okihiro syndrome is characterized by problems with eye movement, bone abnormalities, and even hearing loss.

Treatability 3

Surgery is often necessary for duane anomaly, radial ray malformations, and heart defects.
Hearing aids may be used to improve hearing loss. Growth hormone therapy is recommended for cases of growth retardation.

Penetrance 5

Penetration has been shown to be 95%.

 

Impact

Insufficiently evaluated not reviewed

(The "insufficiently evaluated" qualifier is assigned automatically based on the above evidence and importance scores.)

Inheritance pattern

dominant

Summary of published research, and additional commentary

 

Allele frequency

  • C @ chr20:50407502: 28.1% (3023/10758) in EVS
  • C @ chr20:49840908: 32.8% (42/128) in GET-Evidence
  • Frequency shown in summary reports: 28.1% (3023/10758)

Publications
 

Kohlhase J. SALL4-Related Disorders. 2004 Aug 16 [updated 2008 Mar 12]. In: Pagon RA, Bird TD, Dolan CR, Stephens K, editors. GeneReviews [Internet]. Seattle (WA): University of Washington, Seattle; 1993-. Available from http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=drrs PubMed PMID: 20301547.

“SALL4 – Sal-like 4 (Drosophila).” Genetics Home Reference. Web. 28 Mar. 2011. <http://ghr.nlm.nih.gov/gene/SALL4>.

“Duane-radial Ray Syndrome.” Genetics Home Reference. Web. 28 Mar. 2011. <http://ghr.nlm.nih.gov/condition/duane-radial-ray-syndrome>.

Genomes
 

hu025CEA - CGI sample GS01669-DNA_D02 from PGP sample 27316983
hom C @ chr20:50407502

 

hu0D879F - CGI sample GS00253-DNA_G01_200_37
het C @ chr20:50407502

 

 

hu241DEA - CGI sample GS01175-DNA_D05 from PGP sample 1205491
hom C @ chr20:50407502

 

hu2D6140 - CGI sample GS01173-DNA_F06 from PGP sample 64191565
het C @ chr20:50407502

 

 

hu342A08 - CGI sample GS01175-DNA_B05 from PGP sample 83494370
hom C @ chr20:50407502

 

 

 

hu3CAB43 - CGI sample GS01175-DNA_D03 from PGP sample 27486199
het C @ chr20:50407502

 

hu4040B8 - CGI sample GS01175-DNA_D01 from PGP sample 31286272
hom C @ chr20:50407502

 

hu44DCFF - CGI sample GS01669-DNA_C07 from PGP sample 74521372
hom C @ chr20:50407502

 

hu4CA5B9 - CGI sample GS01669-DNA_B03 from PGP sample 14427241
het C @ chr20:50407502

 

 

 

hu72A81D - CGI sample GS01173-DNA_C02 from PGP sample 10366372
hom C @ chr20:50407502

 

hu92C40A - CGI sample GS01175-DNA_G03 from PGP sample 92527586
het C @ chr20:50407502

 

hu92FD55 - CGI sample GS01669-DNA_A04 from PGP sample 08188426
hom C @ chr20:50407502

 

hu9385BA - CGI sample GS00253-DNA_E01_200_37
hom C @ chr20:50407502

 

huA0E089 - CGI sample GS01175-DNA_B04 from PGP sample 88590671
het C @ chr20:50407502

 

 

huAE6220 - CGI sample GS00253-DNA_H01_200_37
het C @ chr20:50407502

 

huBAAC98 - CGI sample GS01173-DNA_F02 from PGP sample 70008981
het C @ chr20:50407502

 

huC30901 - CGI sample GS00253-DNA_B01_200_37
hom C @ chr20:50407502

 

huD81F3D - CGI sample GS01173-DNA_D06 from PGP sample 69488604
hom C @ chr20:50407502

 

huE80E3D - CGI sample GS00253-DNA_D01_200_37
het C @ chr20:50407502

 

huFAF983 - CGI sample GS01175-DNA_F02 from PGP sample 95788191
hom C @ chr20:50407502

 

GS06994 - var-GS06994-1100-36-ASM
het C @ chr20:49840909

 

GS10851 - var-GS10851-1100-36-ASM
het C @ chr20:49840909

 

GS12004 - var-GS12004-1100-36-ASM
het C @ chr20:49840909

 

GS18505 - var-GS18505-1100-36-ASM
het C @ chr20:49840909

 

GS18526 - var-GS18526-1100-36-ASM
het C @ chr20:49840909

 

GS18537 - var-GS18537-1100-36-ASM
het C @ chr20:49840909

 

GS18555 - var-GS18555-1100-36-ASM
het C @ chr20:49840909

 

GS18558 - var-GS18558-1100-36-ASM
het C @ chr20:49840909

 

GS18940 - var-GS18940-1100-36-ASM
hom C @ chr20:49840909

 

GS18947 - var-GS18947-1100-36-ASM
het C @ chr20:49840909

 

GS18956 - var-GS18956-1100-36-ASM
het C @ chr20:49840909

 

GS19017 - var-GS19017-1100-36-ASM
het C @ chr20:49840909

 

GS19025 - var-GS19025-1100-36-ASM
het C @ chr20:49840909

 

GS19129 - var-GS19129-1100-36-ASM
het C @ chr20:49840909

 

GS19648 - var-GS19648-1100-36-ASM
hom C @ chr20:49840909

 

GS19649 - var-GS19649-1100-36-ASM
het C @ chr20:49840909

 

GS19700 - var-GS19700-1100-36-ASM
het C @ chr20:49840909

 

GS19703 - var-GS19703-1100-36-ASM
het C @ chr20:49840909

 

GS19735 - var-GS19735-1100-36-ASM
het C @ chr20:49840909

 

GS20509 - var-GS20509-1100-36-ASM
het C @ chr20:49840909

 

Other external references
 

    dbSNP
  • rs6126344
    www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi
    PolyPhen-2
  • Score: 0.125 (benign)
    Web search results (12 hits -- see all)
  • Type III 97%
    ... SWISS-PROT ID Variant site Phosphorylation site SWISS-PROT variant ID ... Reference(s) for variant Reference(s) for phosphorylation site TPSD1 Q9BZJ3 P15R ...
    nih.go.kr/phosphovariant/html/family_whole/TypeIII_97.txt

Other in silico analyses
 

  • NBLOSUM100 score = 6
  • GET-Evidence autoscore = 3

Edit history
 

Gene search

"GENE" or "GENE A123C":

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