JUP : c.2089A>T

Variant Details

Variant (CDS)	Variant (protein)	Variant Type	Variant Effect	Genomic Location (GRCh37)	ExAC Frequency
c.2089A>T	p.M697L (Met > Leu)	substitution	missense	chr17:39912145 (reverse strand)	0.65923631

Effect in Cardiac Disease

As this variant is present at a population frequency of 0.65923631 (ExAC mean allelic frequency), it is highly unlikely to be pathogenic.

DCM	OMGL: Detected in 0 / 304 DCM patients. LMM: Detected in 0 / 121 DCM patients.
ARVC	OMGL: Detected in 0 / 94 ARVC patients sequenced at OMGL.

DCM

OMGL: Detected in 0 / 304 DCM patients.

LMM: Detected in 0 / 121 DCM patients.

ARVC

OMGL: Detected in 0 / 94 ARVC patients sequenced at OMGL.

For more information on the clinical significance of this variant, please see the ClinVar entry.

Detection in Population Databases

Database	European	African	East Asian	South Asian	American	Finnish	Other	Total
ExAC	0.72910558 48242 / 66166	0.60370586 6223 / 10308	0.34394682 2949 / 8574	0.73605339 11690 / 15882	0.43059416 4957 / 11512	0.66984077 4291 / 6406	0.65575621 581 / 886	0.65923631 78933 / 119734
ESP	0.73907 6356 / 8600	0.61484 2709 / 4406						0.69699 9065 / 13006
1KG	0.76733 620 / 808	0.57186 756 / 1322	0.34524 348 / 1008	0.74233 726 / 978	0.52305 363 / 694	0.64646 128 / 198		0.58726 2941 / 5008

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

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

0.79121 144 / 182 British	0.57377 70 / 122 African-American	0.30645 57 / 186 Chinese Dai	0.70930 122 / 172 Bengali	0.59574 112 / 188 Colombian
0.77103 165 / 214 Iberian	0.63021 121 / 192 African-Caribbean	0.29126 60 / 206 Han, Beijing	0.76214 157 / 206 Gujarati Indian	0.48438 62 / 128 Mexican, LA
0.72430 155 / 214 Toscani	0.58586 116 / 198 Esan, Nigeria	0.42788 89 / 208 Japanese	0.77451 158 / 204 Indian Telugu	0.39412 67 / 170 Peruvian
0.78788 156 / 198 Utah Europeans	0.53540 121 / 226 Gambian	0.30303 60 / 198 Kinh, Vietnam	0.71875 138 / 192 Punjabi, Lahore	0.58654 122 / 208 Puerto Rican
	0.63131 125 / 198 Luhya, Kenya	0.39048 82 / 210 Southern Han	0.74020 151 / 204 Tamil
	0.53529 91 / 170 Mende
	0.51852 112 / 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	ENST00000393930	LRG_401t2	NM_002230.2
Protein	ENSP00000377507	LRG_401p2		P14923

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)	neutral	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.