Table 3 Molecular features and predicted pathogenicity of DNA variants found in this study
From: Reassessing the pathogenicity of c.2858G>T(p.(G953V)) in COL4A5 Gene: report of 19 Chinese families
DNA variant | Effect on protein | Type | dbSNP reference ID | ClinVar | HGMD | LOVD | 1000 G ASN AF | ExAC AF | SIFT (score) | PolyPhen 2 (score) | Mutation taster | Human splicing finder |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
ADCK4 | ||||||||||||
 c.448C>T | p.(Arg150*) | Nonsense | – | – | – | – | – | – | – | – | DC | – |
 c.748G>C | p.(Asp250His) | Missense | – | – | – | – | – | – | D (0) | PD (1) | DC | – |
NPHS1 | ||||||||||||
 c.3027C>G | p.(Tyr1009*) | Nonsense | rs762184939 | P | DM | – | – | – | – | – | DC | – |
 c.144dup | p.(Val49Serfs*43) | Frameshift | – | – | – | – | – | – | – | – | DC | – |
TRPC6 | ||||||||||||
 c.335C>T | p.(Pro112Leu) | Missense | – | – | a | – | – | – | D (0) | PD (1) | DC | – |
WT1 | ||||||||||||
 c.1432+5G>A | – | Splicing | – | – | DM | – | – | – | – | – | – | SL |
PAX2 | ||||||||||||
 c.418C>T | p.(Arg140Trp) | Missense | – | – | b | – | – | – | D (0) | PD (1) | DC | – |
NPHP1 | ||||||||||||
 c.-94_a455del | – | Large deletion | – | P | DM |  | – | – | – | – | – | – |
COL4A4 | ||||||||||||
 c.4129C>T | p.(Arg1377*) | Nonsense | rs121912861 | P | DM | P | – | 2E−05 | – | – | DC | – |
COL4A5 | ||||||||||||
 c.834+5G>A | – | Splicing | – | P | DM | LP | – | – | – | – | – | SL |
 c.937-2A>C | – | Splicing | – | – | – | – | – | – | – | – | – | SL |
 c.1813_1814dup | p.(Gly606Leufs*13) | Frameshift | – | – | – | – | – | – | – | – | DC | – |
 c.4024G>T | p.(Gly1342*) | Nonsense | – | – | c | – | – | – | – | – | DC | – |
 c.4510delG | p.(Ala1504Profs*50) | Frameshift | – | – | – | – | – | – | – | – | DC | – |
 c.81G>A | p.(Ala27=) | Coding-synon | – | U | – | – | – | – | – | – | DC | SL |
 c.2858G>T | p.(Gly953Val) | Missense | rs78972735 | Ud | DM | U | 0.01 | 0.003 | D (0) | PD (0.99) | Polymorphism | – |
