Table 5.

Predicted functional rare variants in CFHR5

PositionLocationNucleotideAmino AcidIdentified in PopulationdbSNP (Build142)Function Change PredictionSoftware
Chr1:196946445Promoterc.-350G>TPatientsNot transcript elements binding sitesPromoter 2.0
Chr1:196946448Promoterc.-347G>AControlsrs9427942Not transcript elements binding sitesPromoter 2.0
Chr1:196946881Intron 1c.58+29A>CControlsNot branch-point mutationHSF 2.4.1
Chr1:196951903Intron 1c.59–112G>APatientsNot branch-point mutationHSF 2.4.1
Chr1:196953025Intron 2c.254–66A>TPatientsrs570596954Not branch-point mutationHSF 2.4.1
Chr1:196953169Exon 3c.332A>Cp.Gln111ProPatients and controlsTolerated/benignSIFT-Polyphen-2
Chr1:196953379Intron 3c.430+112T>CPatientsNot branch-point mutationHSF 2.4.1
Chr1:196963287Exon 4c.508G>Ap.Val170MetPatients and controlsrs201073457Tolerated/probably damagingSIFT-Polyphen-2
Chr1:196963312Exon 4c.533A>Gp.Asn178SerPatientsrs200427185Damaging/benignSIFT-Polyphen-2
Chr1:196965015Exon 5c.776T>Ap.Leu259TerminationPatientsStop gain
Chr1:196965031Intron 5c.790+2T>CPatientsSplicing siteBDGP, ASSP
Chr1:196965076Intron 5c.790+47A>GPatientsNot branch-point mutationHSF 2.4.1
Chr1:196965183Exon 6c.822A>Tp.Glu274AspPatientsTolerated/benignSIFT-Polyphen-2
Chr1:196967528Intron 7c.1147+94G>TPatients and controlsrs116891819Not branch-point mutationHSF 2.4.1
Chr1:196971491Intron 7c.1148–121G>APatientsNot branch-point mutationHSF 2.4.1
Chr1:196971504Intron 7c.1148–108A>GControlsrs147231103Not branch-point mutationHSF 2.4.1
Chr1:196971544Intron 7c.1148–68C>TControlsrs181464041Not branch-point mutationHSF 2.4.1
Chr1:196971637Exon 8c.1173G>Ap.Pro391ProControlsrs200148491Synonymous mutation
Chr1:196971814Intron 8c.1330+20G>AControlsNot branch-point mutationHSF 2.4.1
Chr1:196971834Intron 8c.1330+40G>AControlsrs116937944Not branch-point mutationHSF 2.4.1
Chr1:196971872Intron 8c.1330+78A>GPatients and controlsNot branch-point mutationHSF 2.4.1
Chr1:196973817Exon 9c.1357C>Tp.Pro453SerControlsrs184883943Tolerated/probably damagingSIFT-Polyphen-2
Chr1:196974101Intron 9c.1513+126A>GPatientsNot branch-point mutationHSF 2.4.1
Chr1:196974110Intron 9c.1513+137G>AControlsrs142743076Not branch-point mutationHSF
Chr1:196977744Exon 10c.1641G>Ap.Ala547AlaPatientsrs74323799Synonymous mutation
Chr1:196977811Exon 10 (stop codon)c.1708T>Cp.Termination570ArgPatients and controlsStop loss
Chr1:1969778163′ UTRc.1710*3C>GPatientsNot microRNA binding siteTargetScanHuman 6.2
Chr1:1969779813′ UTRc.1710*168G>TPatientshsa-mir-2117/hsa-mir-4273 binding siteTargetScanHuman 6.2
  • dbSNP, single nucleotide polymorphism database; —, inapplicable; HSF, Human Splicing Finder; SIFT, Sorting Intolerant from Tolerant; Polyphen-2, Polymorphism Phenotyping v2.