SALL4 : c.2392A>C

SALL4 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.2392A>Cp.I798L (Ile > Leu)substitutionmissense chr20:50406630 (reverse strand)0.05098375

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.05098375 (ExAC mean allelic frequency), it is highly unlikely to be pathogenic.

Detection in Population Databases



Database European African East Asian South Asian American Finnish Other Total
ExAC0.05295581
3533 / 66716		0.16051164
1669 / 10398		0.00103998
9 / 8654		0.02295578
379 / 16510		0.03119599
361 / 11572		0.02857575
189 / 6614		0.05286344
48 / 908		0.05098375
6188 / 121372
ESP 0.05791
498 / 8600		 0.15797
696 / 4406		 0.09180
1194 / 13006
1KG
 0.07054
57 / 808		 0.16188
214 / 1322		 0.00000
0 / 1008		 0.01636
16 / 978		 0.04899
34 / 694		 0.04040
8 / 198		 0.06569
329 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.08242
15 / 182
British
0.20492
25 / 122
African-American
0.00000
0 / 186
Chinese Dai
0.01163
2 / 172
Bengali
0.04255
8 / 188
Colombian
0.06542
14 / 214
Iberian
0.17188
33 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.01456
3 / 206
Gujarati Indian
0.07031
9 / 128
Mexican, LA
0.05607
12 / 214
Toscani
0.17172
34 / 198
Esan, Nigeria
0.00000
0 / 208
Japanese
0.00490
1 / 204
Indian Telugu
0.01765
3 / 170
Peruvian
0.08081
16 / 198
Utah Europeans
0.11062
25 / 226
Gambian
0.00000
0 / 198
Kinh, Vietnam
0.02083
4 / 192
Punjabi, Lahore
0.06731
14 / 208
Puerto Rican
0.18182
36 / 198
Luhya, Kenya
0.00000
0 / 210
Southern Han
0.02941
6 / 204
Tamil
0.11765
20 / 170
Mende
0.18981
41 / 216
Yoruba, Nigeria

The Exome Aggregation Consortium (ExAC) is a database of 60,706 unrelated individuals sequenced as part of various disease-specific and population genetic studies. There is partial overlap between ExAC and 1000 Genomes (1KG) (1,851 of the 2,504 samples in 1KG) and the Exome Sequencing Project (ESP) (3,936 of the 6,500 samples in ESP).


Other Variant & Gene Details

Canonical Sequences
Transcript ENST00000217086 LRG_675t1NM_020436.3
Protein ENSP00000217086 LRG_675p1Q9UJQ4

Missense Variant Predictions
SIFT Grantham Polyphen-DIV Polyphen-VAR Summary
0% of algorithms have predicted that this variant will adversely affect protein function
tolerated conservative benign benign
LRT MutationTaster MutationAssessor FATHMM
neutral polymorphism (auto) low impact tolerated


References

1. Roddy Walsh, Kate L. Thomson, James S. Ware, Birgit H. Funke, Jessica Woodley, Karen J. McGuire, Francesco Mazzarotto, Edward Blair, Anneke Seller, Jenny C. Taylor, Eric V. Minikel, Exome Aggregation Consortium, Daniel G. MacArthur, Martin Farrall, Stuart A. Cook and Hugh Watkins. Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples. Genet Med. 2016 doi:10.1038/gim.2016.90.

2. Pugh TJ, Kelly MA, Gowrisankar S, Hynes E, Seidman MA, Baxter SM, Bowser M, Harrison B, Aaron D, Mahanta LM, Lakdawala NK, McDermott G, White ET, Rehm HL, Lebo M, Funke BH. The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing. Genet Med. 2014 Aug;16(8):601-8.

3. Alfares AA, Kelly MA, McDermott G, Funke BH, Lebo MS, Baxter SB, Shen J, McLaughlin HM, Clark EH, Babb LJ, Cox SW, DePalma SR, Ho CY, Seidman JG, Seidman CE, Rehm HL. Results of clinical genetic testing of 2,912 probands with hypertrophic cardiomyopathy: expanded panels offer limited additional sensitivity. Genet Med. 2015 Nov;17(11):880-8.