catalog rows genes repair-panel hits Neandertal-specific 812 722 12 archaic-specific (Nea+Den) 367 324 2 modern-human-specific 673 571 10 ============================================================================== NEANDERTAL-SPECIFIC -- 12 nonsynonymous changes in the 206-gene repair panel ============================================================================== -- Fanconi anaemia / crosslink repair -- SLX4 chr16:3656625 R/C p.204 PolyPhen=probably_damaging(1) SIFT=deleterious(0) GERP=3.11 flag=CpG archaic alleles (Vin,Sid,Alt,Den)=A/A,A/A,A/A,G/G states=N/N,N/N,N/N,A/A -- double-strand break repair -- ATM chr11:108137940 S/P p.837 PolyPhen=benign(0) SIFT=tolerated(0.15) GERP=1.06 flag=. archaic alleles (Vin,Sid,Alt,Den)=C/C,C/C,C/C,T/T states=N/N,N/N,N/N,A/A BRCA2 chr13:32911273 M/I p.927 PolyPhen=benign(0.011) SIFT=tolerated(0.2) GERP=2.2 flag=. archaic alleles (Vin,Sid,Alt,Den)=A/A,A/A,A/A,G/G states=N/N,N/N,N/N,A/A PALB2 chr16:23632728 Q/R p.1023 PolyPhen=possibly_damaging(0.86) SIFT=tolerated(0.18) GERP=4.19 flag=. archaic alleles (Vin,Sid,Alt,Den)=C/C,C/C,C/C,T/T states=N/N,N/N,N/N,A/A SMC6 chr2 :17881620 S/N p.750 PolyPhen=benign(0) SIFT=tolerated(0.48) GERP=-2.46 flag=. archaic alleles (Vin,Sid,Alt,Den)=T/T,T/T,T/T,C/C states=N/N,N/N,N/N,A/A -- mtDNA replication/maintenance -- TEFM chr17:29226312 D/H p.320 PolyPhen=probably_damaging(0.983) SIFT=deleterious(0) GERP=5.1 flag=. archaic alleles (Vin,Sid,Alt,Den)=G/G,G/G,G/G,C/C states=N/N,N/N,N/N,A/A TOP1MT chr8 :144398285 I/V p.448 PolyPhen=benign(0) SIFT=tolerated(1) GERP=-6.75 flag=. archaic alleles (Vin,Sid,Alt,Den)=C/C,C/C,C/C,T/T states=N/N,N/N,N/N,A/A -- other genome stability -- CLSPN chr1 :36219474 G/D p.548 PolyPhen=benign(0.328) SIFT=tolerated(0.39) GERP=-0.434 flag=. archaic alleles (Vin,Sid,Alt,Den)=T/T,T/T,T/T,C/C states=N/N,N/N,N/N,A/A -- replicative polymerases / proofreading -- POLE chr12:133253995 A/V p.252 PolyPhen=benign(0.007) SIFT=tolerated(0.43) GERP=5.64 flag=. archaic alleles (Vin,Sid,Alt,Den)=A/A,A/A,A/A,G/G states=N/N,N/N,N/N,A/A -- translesion synthesis -- POLH chr6 :43581935 M/V p.595 PolyPhen=benign(0) SIFT=tolerated(0.39) GERP=-6.76 flag=. archaic alleles (Vin,Sid,Alt,Den)=G/G,G/G,G/G,A/A states=N/N,N/N,N/N,A/A POLI chr18:51820571 V/L p.653 PolyPhen=benign(0.441) SIFT=tolerated(0.09) GERP=3.35 flag=. archaic alleles (Vin,Sid,Alt,Den)=C/C,C/C,C/C,G/G states=N/N,N/N,N/N,A/A REV3L chr6 :111628626 V/I p.3064 PolyPhen=benign(0.389) SIFT=deleterious(0.04) GERP=5.71 flag=. archaic alleles (Vin,Sid,Alt,Den)=T/T,T/T,T/T,C/C states=N/N,N/N,N/N,A/A ============================================================================== ARCHAIC-SPECIFIC (NEA+DEN) -- 2 nonsynonymous changes in the 206-gene repair panel ============================================================================== -- Fanconi anaemia / crosslink repair -- FANCA chr16:89839766 P/A p.643 PolyPhen=benign(0.001) SIFT=tolerated(0.29) GERP=-2.44 flag=. archaic alleles (Vin,Sid,Alt,Den)=C/C,C/C,C/C,C/C states=N/N,N/N,N/N,N/N -- double-strand break repair -- BARD1 chr2 :215617178 C/S p.557 PolyPhen=benign(0.04) SIFT=tolerated(0.64) GERP=2.03 flag=. archaic alleles (Vin,Sid,Alt,Den)=G/G,G/G,G/G,G/C states=N/N,N/N,N/N,N/A ============================================================================== MODERN-HUMAN-SPECIFIC -- 10 nonsynonymous changes in the 206-gene repair panel ============================================================================== -- Fanconi anaemia / crosslink repair -- FANCI chr15:89838293 D/E p.868 PolyPhen=benign(0) SIFT=tolerated(0.75) GERP=2.93 flag=. archaic alleles (Vin,Sid,Alt,Den)=C/A,C/A,A/A,A/A states=A/H,A/H,H/H,H/H SLX4 chr16:3647692 K/N p.457 PolyPhen=benign(0) SIFT=tolerated(1) GERP=5.19 flag=. archaic alleles (Vin,Sid,Alt,Den)=C/C,C/C,C/C,C/C states=A/A,A/A,A/A,A/A -- base-excision repair (the mtDNA repair pathway) -- LIG1 chr19:48639022 V/M p.480 PolyPhen=benign(0) SIFT=tolerated(1) GERP=3.92 flag=CpG archaic alleles (Vin,Sid,Alt,Den)=C/C,T/T,T/T,T/T states=A/A,H/H,H/H,H/H -- double-strand break repair -- BRCA2 chr13:32911463 D/N p.991 PolyPhen=benign(0) SIFT=tolerated(1) GERP=3.08 flag=. archaic alleles (Vin,Sid,Alt,Den)=G/G,G/G,G/G,A/A states=A/A,A/A,A/A,H/H NHEJ1 chr2 :219942814 T/A p.235 PolyPhen=benign(0) SIFT=tolerated(1) GERP=-4.05 flag=CpG archaic alleles (Vin,Sid,Alt,Den)=T/T,T/T,T/T,C/C states=A/A,A/A,A/A,H/H -- helicases / progeroid -- ZMPSTE24 chr1 :40726647 I/T p.87 PolyPhen=benign(0) SIFT=tolerated(1) GERP=3.57 flag=. archaic alleles (Vin,Sid,Alt,Den)=C/C,C/C,C/C,T/T states=H/H,H/H,H/H,A/A -- mismatch repair -- EXO1 chr1 :242045275 R/C p.723 PolyPhen=possibly_damaging(0.767) SIFT=tolerated(0.13) GERP=1.84 flag=CpG archaic alleles (Vin,Sid,Alt,Den)=C/C,C/C,C/C,C/C states=A/A,A/A,A/A,A/A -- nucleotide-excision repair -- ERCC5 chr13:103527849 G/R p.1053 PolyPhen=benign(0.283) SIFT=deleterious(0.03) GERP=4.28 flag=. archaic alleles (Vin,Sid,Alt,Den)=C/C,C/C,C/C,G/C states=H/H,H/H,H/H,A/H ERCC5 chr13:103527930 G/R p.1080 PolyPhen=benign(0.001) SIFT=tolerated(0.52) GERP=0.141 flag=. archaic alleles (Vin,Sid,Alt,Den)=C/C,C/C,C/C,G/C states=H/H,H/H,H/H,A/H -- replicative polymerases / proofreading -- POLD3 chr11:74347299 V/L p.393 PolyPhen=benign(0) SIFT=tolerated(1) GERP=-2.42 flag=. archaic alleles (Vin,Sid,Alt,Den)=G/G,G/G,G/C,G/G states=A/A,A/A,A/H,A/A