SALL4 : c.1520T>G

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.1520T>G	p.L507R (Leu > Arg)	substitution	missense	chr20:50407502 (reverse strand)	0.35056334

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.35056334 (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
ExAC	0.34914375 23283 / 66686	0.14522379 1499 / 10322	0.59879546 5170 / 8634	0.41803974 6901 / 16508	0.27964051 3236 / 11572	0.31599637 2090 / 6614	0.35761589 324 / 906	0.35056334 42503 / 121242
ESP	0.34384 2957 / 8600	0.14980 660 / 4406						0.27810 3617 / 13006
1KG	0.33292 269 / 808	0.12179 161 / 1322	0.59623 601 / 1008	0.47342 463 / 978	0.33862 235 / 694	0.34343 68 / 198		0.35883 1797 / 5008

View sub-population details for 1000 Genomes (1KG) data

Hide sub-population details for 1000 Genomes (1KG) data

0.31868 58 / 182 British	0.13115 16 / 122 African-American	0.60753 113 / 186 Chinese Dai	0.52326 90 / 172 Bengali	0.37234 70 / 188 Colombian
0.41589 89 / 214 Iberian	0.12500 24 / 192 African-Caribbean	0.57767 119 / 206 Han, Beijing	0.41262 85 / 206 Gujarati Indian	0.32031 41 / 128 Mexican, LA
0.35047 75 / 214 Toscani	0.06566 13 / 198 Esan, Nigeria	0.54327 113 / 208 Japanese	0.47549 97 / 204 Indian Telugu	0.24706 42 / 170 Peruvian
0.23737 47 / 198 Utah Europeans	0.19027 43 / 226 Gambian	0.66162 131 / 198 Kinh, Vietnam	0.41667 80 / 192 Punjabi, Lahore	0.39423 82 / 208 Puerto Rican
	0.19192 38 / 198 Luhya, Kenya	0.59524 125 / 210 Southern Han	0.54412 111 / 204 Tamil
	0.05294 9 / 170 Mende
	0.08333 18 / 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_675t1	NM_020436.3
Protein	ENSP00000217086	LRG_675p1		Q9UJQ4

Missense Variant Predictions
SIFT	Grantham	Polyphen-DIV	Polyphen-VAR	Summary 25% of algorithms have predicted that this variant will adversely affect protein function
tolerated	moderately radical	benign	benign
LRT	MutationTaster	MutationAssessor	FATHMM
neutral	polymorphism (auto)	medium 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.