TableS1: List of variants confirmed to be true by Sanger sequencing with scoring from 0-3
Gene
Mutation
Num
ber
of
samp
le#
Affect all
gene
transcripts
Impact
on >10
% of
the
ORF
score
OMIM phenotype
?[Birbeck granule deficiency [MIM
613393]
Charcot-Marie-Tooth disease, type 1F
[MIM 7734]
Charcot-Marie-Tooth disease, type 2E
[MIM 607684]
Enhanced S-cone syndrome [MIM
268100 ]
Retinitis pigmentosa 37 [MIM
611131]
Van den Ende-Gupta syndrome [MIM
600920]
Predicted to have no effect on the
transcript/ Intronic_exonic boundary
Predicted to have no effect on the
transcript/ Intronic_exonic boundary
Glycogen storage disease Ib [MIM
232220]
Glycogen storage disease Ic [MIM
232240]
Pseudovaginal perineoscrotal
hypospadias [MIM 264600]
5-oxoprolinase deficiency [MIM
260005]
Bowen-Conradi syndrome [MIM
211180]
[MIM 607450, 605676, 615821,
609638, 612908, 607655]
Predicted to have no effect on the
transcript/ Intronic_exonic boundary
Retinitis pigmentosa 69 [MIM
615780]
Genomic annotation error/ Intronic
exonic boundary predicted to have no
effect on the transcript
CD207
NM_015717:c.73_74insG:p.E25fs,
414
0
NEFL
NM_006158:c.1414delC:p.L472fs,
123
0
NR2E3
NM_014249:c.948delC:p.D316fs
112
0
SCARF2
NM_182895:c.2288_2289insC:p.A763fs
NM_182895:c.2238_2239insG:p.A746fs
NM_182895:c.2233_2234insG:p.A745fs
NM_182895:c.2290_2291insC:p.E764fs
35
0
SLC37A4
NM_001164278:c.528delG:p.W176fs
123
0
SRD5A2
NM_000348:c.90_91insC:p.P30fs,
90
0
OPLAH
33
0
EMG1
NM_017570:c.3501_3502del:p.1167_116
8del
NM_006331:c.124_125insG:p.S42fs
118
0
DSP
NM_001008844:c.1_2insA:p.M1fs
5
0
PLK1S1
NM_001163022:c.1075_1076insG:p.R359f
s
123
0
Note
Predicted to have no effect on the
transcript/ Intronic_exonic boundary
Genome annotation error
Predicted to have no effect on the
transcript/ Intronic_exonic boundary
Predicted to have no effect on the
transcript/ Intronic_exonic boundary
Genomic annotation error
Changing the start codon ATG to AATG
which will still read as A_ATG
Combined hyperlipidemia, familial
[MIM 144250]
Lipoprotein lipase deficiency [MIM
238600]
Deafness, autosomal dominant 11
[MIM [601317]
Deafness, autosomal recessive 2
[MIM 600060]
Usher syndrome, type 1B [MIM
276900]
Aicardi-Goutieres syndrome 2 [MIM
610181]
LPL
NM_000237.2:c.1421C>G ; p.Ser474*
7
no
no
1
MYO7A
NM_001127179.2:c.3515_3536del;
p.Gly1172Glufs*34
68
no
no
1
RNASEH2B
NM_024570.3: c.925dup; p.Ile309Asnfs*8
2
no
no
1
TREH
NM_007180.2:c.1706dupC :
p.Ala570Glyfs*35
122
no
no
1
Trehalase deficiency [MIM 612119]
ABHD12
NM_001042472.2:c.1189C>T; p.Gln397*
1
no
no
1
No phenotype associated with the
respective OMIM phenotype.
SETBP1
NM_001130110.1:c.681_682insTCTT
;p.Thr228Serfs*8
123
no
no
1
ANTXR2
NM_058172.5:c.1450C>T: p.Arg484*
1
no
no
1
H6PD
NM_001282587.1:c.-7-0delCCCAGGCA
7
no
yes
2
LFNG
NM_001166355.1: c.163_166dup
16
no
yes
2
Polyneuropathy, hearing loss, ataxia,
retinitis pigmentosa, and cataract
[MIM 612674]
Mental retardation, autosomal
dominant 29 [MIM 616078 ]/
Schinzel-Giedion midface retraction
syndrome [MIM 269150]
Hyaline fibromatosis syndrome [MIM
228600 ]
Cortisone reductase deficiency 1
[MIM 604931]
?Spondylocostal dysostosis 3,
autosomal recessive [MIM 609813]
Amyloidosis, primary localized
cutaneous, 1/ Autosomal dominant
Ichthyosis, congenital, autosomal
recessive 10 [ 615024]
Mitochondrial DNA depletion
syndrome 8A and B [MIM 612075]
Progressive external ophthalmoplegia
with mitochondrial DNA deletions,
No phenotype associated with the
respective OMIM phenotype
No phenotype associated with the
respective OMIM phenotype
No phenotype associated with the
respective OMIM phenotype
p.Glu56Glyfs*2
OSMR
NM_003999.2:c.1207C>T; p.Arg403Ter
1
no
yes
2
PNPLA1
NM_001145716.2:c.1206T>A; p.Tyr402*
1
yes
no
2
RRM2B
NM_001172477.1:c.211dup ;
p.Arg71Profs*28
1
no
yes
2
No phenotype associated with the
respective OMIM phenotype
Phenotype could not be assessed _early
death
autosomal dominant, 5 [MIM
613077]
TGIF1
NM_170695.3:c.246delT;
p.Pro83Leufs*51
41
no
yes
2
Holoprosencephaly-4 [MIM 602630]
LTBP4
NM_001042544.1:c.3236dupG;
p.Tyr1080Leufs*17
120
no
yes
2
Cutis laxa, autosomal recessive, type
IC [MIM 613177]
TMPRSS15
NM_002772.2:c.2808_2809insATCA;
p.Ser937Ilefs*4
1
yes
no
2
Enteropeptidase deficiency [MIM
226200]
Phenotype could not be assessed _early
death
AMPD1
NM_000036.2:c.133C>T ;p.Gln45*
2
no
yes
2
AMT
NM_001164711.1:c.814dup;
p.Ala272Glyfs*22
NM_001081563.2:c.1691dup;
p.Ala565Glyfs*28
1
no
yes
2
1
no
yes
2
Myopathy due to myoadenylate
deaminase deficiency [MIM 615511]
Glycine encephalopathy [MIM
605899]
Myotonic dystrophy 1 [MIM 160900]
CDH15
NM_004933.2: c.2088_2089del;
p.His697Profs*20
1
no
yes
2
Mental retardation, autosomal
dominant 3 [MIM 612580]
No phenotype associated with the
respective OMIM phenotype
Phenotype could not be assessed _early
death
Reported mutations in this gene only as
repeat variation/Autosomal dominant
No phenotype associated with the
respective OMIM phenotype
No phenotype associated with the
respective OMIM phenotype
CCDC39
NM_181426.1:c.2660dupT;
p.Ser888Ilefs*6
1
yes
no
2
Ciliary dyskinesia, primary, 14 [MIM
613807]
No phenotype associated with the
respective OMIM phenotype
COQ6
NM_182480.2:c.41G>A; p.Trp14*
1
no
yes
2
CC2D2A
NM_020785.2: c.262C>T; p.Arg88*
2
No
yes
2
No phenotype associated with the
respective OMIM phenotype
No phenotype associated with the
respective OMIM phenotype
FLG
NM_002016.1:c.12181G>T; p.Glu4061*
1
yes
no
2
ALG9
NM_024740.2:c.61del;p.Ala21Profs*55
75
no
yes
2
PRSS12
NM_003619.3:c.2323C>T : p.Arg775*
1
yes
yes
3
Coenzyme Q10 deficiency, primary, 6
[MIM 614650]
COACH syndrome [MIM 216360]
Joubert syndrome 9 [MIM 612285]
Meckel syndrome 6 [MIM 612284]
Ichthyosis vulgaris [MIM 146700]
Dermatitis, atopic, susceptibility to, 2
[MIM 605803]
Congenital disorder of glycosylation,
type Il [MIM 608776 ]
Mental retardation, autosomal
recessive 1 [MIM 249500]
DMPK
Phenotype could not be assessed _early
death
See Table 1 and text
Erythrokeratodermia variabilis with
erythema gyratum repens/ Deafness
[MIM 133200]
Spermatogenic failure 14 [MIM
615842]
Ichthyosis, congenital [MIM 613943]
See Table 1 and text
3
Poikiloderma, hereditary fibrosing,
with tendon contractures, myopathy,
and pulmonary fibrosis [MIM
615704]
See Table 1 and text
yes
3
Spinocerebellar ataxia 23 [MIM
610245]
See Table 1 and text
yes
yes
3
Familial cold autoinflammatory
syndrome 2 [MIM 611762]
See Table 1 and text
1
yes
yes
3
Hyperglycinuria [MIM 138500]
See Table 1 and text
40
yes
yes
3
10
yes
yes
3
ABCG5
NM_022436.2:c.1336C>T: p.Arg446*
1
yes
yes
3
Hypomagnesemia 3, renal [MIM
248250]
Night blindness, congenital stationary
(complete), 1C, [MIM 613216]
Sitosterolemia [MIM 210250
See Table 1 and text
TRPM1
NM_006580.3:c.166delG;
p.Ala56Leufs*16
NM_001252020.1:c.4240G>T; p.Glu1414*
GJB4
NM_153212.2: c.155_158del;
p.Val52Alafs*55
1
yes
yes
3
ZMYND15
NM_001267822.1: c.1024dupC;
p.Leu342Profs*4
NM_001102469.1:c.302delG;
p.Gly101Glufs*7
1
yes
yes
3
3
yes
yes
3
FAM111B
NM_198947.3:c.394delT:
p.Tyr132Metfs*6
2
yes
yes
PDYN
NM_001190899.2:c.34delC;
p.Leu12Serfs*20
2
yes
NLRP12
NM_144687.3: c.1854C>G; p.Tyr618*
1
SLC36A2
NM_181776.2:c.1010G>A; p.Trp337*
CLDN16
LIPN
See Table 1 and text
See Table 1 and text
See Table 1 and text
See Table 1 and text
Score 3: Variants affect all gene transcripts and >10% of the ORF. Score 2: Variant either affect >10% of the ORF or affect all gene transcripts.
Score 1: variants affect the last 10% of the ORF and only in a subset of the gene’s transcripts. Score 0: Variants with annotation error or
predicted to be non LOF. # No of samples in which this variant confirmed by Sanger sequencing to present in homozygous state.