C1539F Summary

SCN5A C1539F was found in 0 papers (see below) with a total of 1 carrier: 0 had BrS1, 0 had LQT3, and 0 had other disease. C1539F is present in 1 out of 249246 alleles in gnomAD (minor allele frequency of 0.000401%). C1539F has been functionally characterized in 0 papers. Other variants at the same resdue are C1539F .C1539G .C1539R .C1539S .C1539S .C1539W .C1539Y . This residue is located in a Non_Hotspot region for BrS1 and in a Non_Hotspot region for Long QT syndrome.

C1539F Predictions

PROVEAN scores less than -2 are considered deleterious. REVEL scores higher than 0.5 or 0.75 is considered likely pathogenic (higher sensitivity with the former cutoff, higher specificity with the latter cutoff). A PolyPhen-2 score of 0.85 or greater is considered likely pathogenic. PAM scores reflect the chemistry difference between WT and variant amino acid (more negative being greater difference between the two). BLAST-PSSM reflects the evolutionary conservation of residue substitutions, more negative numbers indicate fewer observations of the specific substitution than is expected.

SIFT Sift Score PROVEAN Score Polyphen2 Polyphen2 Score eaRate blastPssm pamScore REVEL
Damaging 0 -9.39 probablydamaging 0.998 1.781 1.22 -13 0.84

C1539F has 53 neighbors within 15 ångströms that have been found in individuals.

A residue within a folded protein on average has nearest neighbors that fall roughly into two shells: a "nearest" neighbor around 5-6 angstroms and a second shell around 11 angstroms.

ResidueNumber Distance(Å) Variants
255 14.4
256 14.9
258 13.5
259 9.7
260 13.6
262 10.6
263 10.9 V263I
265 14.5
266 11.8
267 14.8
358 14.4
1529 14.5
1530 14.2
1531 12.6
1532 10.2 V1532F V1532I
1533 10 T1533I
1534 9
1535 6.3
1536 5.6
1537 6.3
1538 4.4
1540 4.9
1541 6.7
1542 5.6
1543 6.9 V1543A V1543L V1543L
1544 9.6
1545 10.4
1546 10.1
1547 13.7
1563 13.2
1564 13.6
1566 14.2
1567 10.2
1568 14.6
1570 13.1 p.1570_F1571insI p.I1570dup
1571 11.4
1574 13.7 E1574K
1591 14.1
1595 13.5
1598 14.9
1625 14.9
1626 11.2 R1626C R1626H R1626P
1627 10.1
1628 11.5
1629 9.4 R1629G R1629Q
1630 6.6
1631 10.2 G1631D
1632 9.4 R1632C R1632H
1633 8.4
1634 12.8
1635 13.3
1636 10.8
1637 14.3