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Table 2 Filtered variants from whole-genome analysis. Variants with predicted high or moderate effects and a homozygous mutant genotype exclusively found in the LS-affected pool as well as a heterozygous or homozygous wild-type genotype in the LS-unaffected pool are shown. All five reference dogs of four different breeds do not show the mutant genotype. Potential functional effects of these variants were predicted using SIFT and PolyPhen

From: Variant detection and runs of homozygosity in next generation sequencing data elucidate the genetic background of Lundehund syndrome

CFA Position Base change Amino acid change Consequence Genotype (LS-affected Lunde-hund pool) Genotype (LS-unaffected Lunde-hund pool) Genotype (5 reference dogs) Gene (transcript) SIFT PolyPhen-2
1 13398018 T>G T>P/ S>R missense variant 1/1 0/0 0/0 ENSCAFG00000031329 (novel gene; (ENSCAFT00000043665) and ENSCAFG00000030129 (novel gene; ENSCAFT00000048679) tolerated (0.07)/ deleterious (0.02) benign (0.074)/-
1 111903572 A>G T>A missense variant 1/1 0/1 0/0 CEACAM1 (ENSCAFT00000007749/ ENSCAFT00000046087/ ENSCAFT00000022623/ ENSCAFT00000047331/ ENSCAFT00000049292) tolerated (0.08/ 0.13/ 0.2/ 0.21/ 0.2) benign (0.00)/ benign (0.310)/ possibly damaging (0.659)/ possibly damaging (0.605)/ benign (0.250)
3 56483857 G>T P>T missense variant 1/1 0/1 0/0 IL16 (ENSCAFT00000021964) tolerated (0.59) benign (0.310)
3 62265062 A>T F>I missense variant 1/1 0/1 0/0 ENSCAFG00000017475 (novel gene; ENSCAFT00000027691) deleterious (0.01) possibly damaging (0.614)
5 16233038 G>T L>M missense variant 1/1 0/1 0/0 CEP164 (ENSCAFT00000020686) deleterious (0.02) probably damaging (0.996)
6 67204999 C>T R>Q non coding transcript variant 1/1 0/1 0/0 ENSCAFG00000005648 (novel gene; ENSCAFT00000009086) - -
6 67205308 A>C Y>* (stop codon) non coding transcript variant 1/1 0/1 0/0 ENSCAFG00000005648 (novel gene; ENSCAFT00000009086) - -
6 67205754 G>A R>* (stop codon) non coding transcript variant 1/1 0/1 0/0 ENSCAFG00000005648 (novel gene; ENSCAFT00000009086) - -
6 67205959 A>G L>P non coding transcript variant 1/1 0/1 0/0 ENSCAFG00000005648 (novel gene; ENSCAFT00000009086) - -
6 67205966 T>G T>P non coding transcript variant 1/1 0/1 0/0 ENSCAFG00000005648 (novel gene; ENSCAFT00000009086) - -
7 2590167 G>A S>N missense variant 1/1 0/1 0/0 KIF14 (ENSCAFT00000017720) tolerated (0.21) benign (0.002)
7 4169250 A>T F>Y missense variant 1/1 0/1 0/0 PTPRC (ENSCAFT00000017964/ ENSCAFT00000017955) tolerated (0.3/ 0.31) benign (0.023/
0.347 )
8 22616300 C>T P>L missense variant 1/1 0/1 0/0 FANCM (ENSCAFT00000046644/ ENSCAFT00000022327/ ENSCAFT00000048988) tolerated (0.42/ 0.34/ 0.42) benign (0.009/ 0.009/ 0.004 )
8 47544408 G>A G>R missense variant 1/1 0/1 0/0 VRTN (ENSCAFT00000026784) tolerated (0.56) possibly damaging (0.560)
8 73685892 C>G Q>H missense variant 1/1 0/1 0/0 ENSCAFG00000029996 (novel gene; ENSCAFT00000049952) deleterious (0) benign (0.152)
8 73685923 C>G W>S missense variant 1/1 0/1 0/0 ENSCAFG00000029996 (novel gene; ENSCAFT00000049952) deleterious (0) probably damaging (1.000)
8 73685927 T>G S>R missense variant 1/1 0/1 0/0 ENSCAFG00000029996 (novel gene; ENSCAFT00000049952) tolerated (0.21) probably damaging (0.963)
9 37739213 C>T R>W missense variant 1/1 0/1 0/0 ENSCAFG00000032731 (novel gene; ENSCAFT00000047013) tolerated (0.07) probably damaging (0.998)
9 51227945 T>C H>R missense variant 1/1 0/1 0/0 ENSCAFG00000019863 (novel gene; ENSCAFT00000031603) deleterious (0) possibly damaging (0.898)
10 36330685 C>T A>V missense variant 1/1 0/1 0/0 FAM32A (ENSCAFT00000003279) tolerated (0.16) benign (0.328)
11 67454670 A>C S>R missense variant 1/1 0/1 0/0 ENSCAFG00000028946
(novel gene; ENSCAFT00000045538)
tolerated (0.33) -
12 40430108-40430109 A>AGG R47fs frameshift variant 1/1 0/1 0/0 ENSCAFG00000030790 (novel gene; ENSCAFT00000045206) - -
12 52354031 A>G F>S missense variant 1/1 0/1 0/0 ENSCAFG00000030881 (novel gene;
ENSCAFT00000046435)
deleterious (0.01) -
12 52354041 G>A L>F missense variant 1/1 0/1 0/0 ENSCAFG00000030881 (novel gene;
ENSCAFT00000046435)
deleterious (0.02) -
14 16187782 T>G I>M missense variant 1/1 0/1 0/0 CFAP69 (ENSCAFT00000002973) tolerated (0.23) possibly damaging (0.648)
14 22993351 A>T C>S missense variant 1/1 0/1 0/0 COL28A1 (ENSCAFT00000044570) deleterious (0) probably damaging (1.000)
18 39577830 C>T A>V missense variant 1/1 0/1 0/0 ENSCAFG00000030998 (novel gene; ENSCAFT00000047197) tolerated (1) benign (0.000)
20 54722514
rs22884799
T>C I>M missense variant 1/1 0/1 0/0 KDM4B (ENSCAFT00000030040) tolerated (0.7) possibly damaging (0.728)
27 2322565 C>T R>C missense variant 1/1 0/1 0/0 KRT3 (ENSCAFT00000011634) deleterious (0.03) possibly damaging (0.942)
28 31706107 A>C N>T missense variant 1/1 0/1 0/0 ENSCAFG00000012412 (novel gene; (ENSCAFT00000019700) tolerated (0.78) benign (0.000)
32 21555092 C>T D>N missense variant 1/1 0/1 0/0 TRMT10A (ENSCAFT00000016732) tolerated (0.31) probably damaging (0.997)
34 22046092 C>G E>Q missense variant 1/1 0/1 0/0 LEPREL1 (ENSCAFT00000022188) tolerated (0.43) possibly damaging (0.945)
X 96702059
rs24643372
A>G R>G missense variant 1/1 0/1 0/0 ENSCAFG00000029138 (novel gene; ENSCAFT00000044717) tolerated (0.41) benign (0.001)
  1. * is the official HGVS-symbol for a stop codon