PTPN11 : c.1093-9C>A

PTPN11 gene summary

Variant Details

Variant (CDS)Variant (protein)Variant Type Variant EffectGenomic Location (GRCh37)ExAC Frequency
c.1093-9C>Asubstitutionsplice site chr12:112919869 (forward strand)0.01978147

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.01978147 (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
ExAC0.01051858
701 / 66644		0.11752717
1211 / 10304		0.00821569
71 / 8642		0.00969110
160 / 16510		0.01280498
148 / 11558		0.01406959
93 / 6610		0.01434879
13 / 906		0.01978147
2397 / 121174
ESP 0.00000
0 / 8600		 0.00000
0 / 4400		 0.00000
0 / 13000
1KG
 0.00866
7 / 808		 0.13389
177 / 1322		 0.00893
9 / 1008		 0.00613
6 / 978		 0.01873
13 / 694		 0.01515
3 / 198		 0.04293
215 / 5008
View sub-population details for 1000 Genomes (1KG) data
Hide sub-population details for 1000 Genomes (1KG) data

0.00549
1 / 182
British
0.09016
11 / 122
African-American
0.02688
5 / 186
Chinese Dai
0.00581
1 / 172
Bengali
0.04255
8 / 188
Colombian
0.01869
4 / 214
Iberian
0.11458
22 / 192
African-Caribbean
0.00000
0 / 206
Han, Beijing
0.00485
1 / 206
Gujarati Indian
0.00781
1 / 128
Mexican, LA
0.00467
1 / 214
Toscani
0.11616
23 / 198
Esan, Nigeria
0.00962
2 / 208
Japanese
0.00490
1 / 204
Indian Telugu
0.00588
1 / 170
Peruvian
0.00505
1 / 198
Utah Europeans
0.15929
36 / 226
Gambian
0.00000
0 / 198
Kinh, Vietnam
0.00521
1 / 192
Punjabi, Lahore
0.01442
3 / 208
Puerto Rican
0.19697
39 / 198
Luhya, Kenya
0.00952
2 / 210
Southern Han
0.00980
2 / 204
Tamil
0.10588
18 / 170
Mende
0.12963
28 / 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 ENST00000351677 LRG_614t1NM_002834.3
Protein ENSP00000340944 LRG_614p1



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.