Table 2.

New HLA-I–restricted MiHAs identified by GWAS

HLAMiHASequence∗ SNPHLA-alleleEuropean population allele frequency† Type of transcript encoding MiHA
Common HLAs 
A∗01:01 LB-LINC01857-1D ST[D/N]ESVLSDY rs1055228 A∗01:01 0.43 lncRNA ORF 
LB-OAS1-1R ETDDPR[R/T]YQKY rs1051042 A∗01:01 0.34 Annotated ORF 
LB-SLC35B1-1H RVD[H/R]TRSWLY rs1135034 A∗01:01 0.09 Annotated ORF 
LB-UAP1L1-1A R[A/V]SDGSLLY rs7037849 A∗01:01 0.60 Annotated ORF 
A∗02:01 LB-DHX38-1W ALHY[W/S]DWTC rs1050361 A∗02:01 0.40 Out-of-frame ORF 
LB-E2F2-1H ALD[H/Q]LIQSC rs2075995 A∗02:01 0.51 Annotated ORF 
LB-LINC02427-1G FLWLGAPP[G/S]M rs1991229 A∗02:01 0.26 lncRNA ORF 
LB-MIS18BP1-1Q K[Q/E]FPITEAV rs34402741 A∗02:01 0.01 Annotated ORF 
LB-MTHFD1-1Q SIIAD[Q/R]IAL rs2236225 A∗02:01 0.43 Annotated ORF 
LB-NDUFAF1-1H KLL[H/R]GTYFL rs1899 A∗02:01 0.27 Annotated ORF 
LB-SLAMF1-1F GLLSLT[F/L]VL rs2295612 A∗02:01 0.78 Annotated ORF 
LB-SSR1-2L VLFRGGPRG[L/S]LAVA rs10004 A∗02:01 0.75 Annotated ORF 
LB-TIAM2-1C RL[C/R]KVIQEL rs11751128 A∗02:01 0.27 Annotated ORF 
A∗03:01 LB-APOBEC3B-3K QVYF[K/E]PQYH rs2076109 A∗03:01 0.40 Annotated ORF 
LB-APOBEC3H-2R [R/G]IFASRLYY rs139297 A∗03:01 0.46 Annotated ORF 
LB-EXO1-1R [R/H]SWDDKTCQK rs735943 A∗03:01 0.57 Annotated ORF 
LB-F13A1-1L ITFYTGV[L/P]K rs5982 A∗03:01 0.21 Annotated ORF 
LB-KLHDC9-1R RLDP[R/S]ARTY rs11576830 A∗03:01 0.34 Annotated ORF 
LB-MCM10-1R RA[R/K]GQVLTK rs2274110 A∗03:01 0.19 Annotated ORF 
LB-NANS-1D KAL[D/E]RPYTSK rs1058446 A∗03:01 0.22 Annotated ORF 
LB-SLC5A6-1F SL[F/L]PLSCQK rs61737373 A∗03:01 0.07 Annotated ORF 
B∗07:02 LB-APOBEC3B-4L TPC[L/P]DCVAKL rs2076110 B∗07:02 0.06 Annotated ORF 
LB-APOBEC3H-1K KPQQ[K/D]GLRLL rs139298, rs139299 B∗07:02 0.52 Annotated ORF 
LB-CYTOR-1W RPLHL[W/R]VVCL rs7657 B∗07:02 0.45 lncRNA ORF 
LB-DDX20-1R TPVDD[R/S]ISL rs197414 B∗07:02 0.87 Annotated ORF 
LB-DHX37-1R KLASY[R/Q]SCL rs4447263 B∗07:02 0.40 Annotated ORF 
LB-DOK2-1L LPRPDSPYSR[L/P] rs34215892 B∗07:02 0.03 Annotated ORF 
LB-ERGIC1-1R [R/G]PWPPTLLL rs477748 B∗07:02 0.29 Alternative transcript 
LB-FANCA-1S VP[S/G]KYRSLL rs2239359 B∗07:02 0.41 Annotated ORF 
LB-FBXO7-1E RPP[E/G]GSGPLL rs9621461 B∗07:02 0.09 Out-of-frame ORF 
LB-HNRNPUL1-1R LPSNSR[R/H]HSSL rs1056854 B∗07:02 0.17 Out-of-frame ORF 
LB-IGSF3-1R SP[R/Q]DTGNYSC rs6703791 B∗07:02 0.17 Annotated ORF 
LB-IL10RA-1R GPRWPP[R/Q]MTH rs2256111 B∗07:02 0.51 Out-of-frame ORF 
LB-KIAA0040-1L HPFE[L/P]RTCL rs1057239 B∗07:02 0.44 Upstream ORF 
LB-LGALS3-1H KPFKI[H/Q]VL rs11125 B∗07:02 0.08 Annotated ORF 
LB-LILRB4-1G [G/D]PRPSPTRSV rs731170 B∗07:02 0.70 Annotated ORF 
LB-LTA-1R RV[R/C]GTTLHLLL rs2229094 B∗07:02 0.29 Annotated ORF 
LB-MKI67-1Q [Q/R]PRAPRESA rs10764749 B∗07:02 0.27 Annotated ORF 
LB-MRPS34-1I RPRDSQ[I/L]YA rs11552431 B∗07:02 0.13 Annotated ORF 
LB-MYO3B-1R AP[R/H]SGWPLRSL rs2161916 B∗07:02 0.44 Out-of-frame ORF 
LB-NUP210-1A [A/V]PVYTSPQL rs6795271 B∗07:02 0.68 Annotated ORF 
LB-PDCD11-2L GPDSSKT[L/F]LCL rs2986014 B∗07:02 0.58 Annotated ORF 
LB-PFAS-1P A[P/S]GHTRRKL rs9891699 B∗07:02 0.17 Annotated ORF 
LB-PPP6R1-1P MPWV[P/L]MSPF rs3745920 B∗07:02 0.34 Out-of-frame ORF 
LB-RPS6KB2-1V SPR[V/A]PVSPLKF rs13859 B∗07:02 0.42 Annotated ORF 
LB-SIK1-1A [A/V]PASRASRGGL rs430554 B∗07:02 0.12 Annotated ORF 
LB-SRP14-1 LPMGRRRSALW rs1059395 B∗07:02 0.18 Out-of-frame ORF 
LB-TXNDC11-1P R[P/L]RGLRLPQL rs3743588 B∗07:02 0.74 Out-of-frame ORF 
LB-TYMSOS-1G RPLP[G/R]RIEV rs2853533 B∗07:02 0.15 lncRNA ORF 
LB-UBE2G2-1R [R/G]PRVAGGLSVC rs7364120 B∗07:02 0.29 Alternative transcript 
LB-USP15-1I MPSHLRN[I/T]LL rs11174420 B∗07:02 0.31 Out-of-frame ORF 
LB-USP15-2T MPSHLRN[T/I]LLM rs11174420 B∗07:02 0.69 Out-of-frame ORF 
LB-ZNF419-2G IPR[G/D]SWWVEL rs2074071 B∗07:02 0.69 Annotated ORF 
B∗08:01 LB-AP3B1-1V VPN[V/E]KSGAL rs6453373 B∗08:01 0.07 Annotated ORF 
LB-ARHGEF39-1R SFP[R/H]EKLLLM rs2297879 B∗08:01 0.33 Annotated ORF 
LB-C12ORF57-1A L[A/V]FYRKAPL rs7965269 B∗08:01 0.70 Upstream ORF 
LB-DEPDC1-1R HLFE[R/Q]ECL rs78030459 B∗08:01 0.05 Out-of-frame ORF 
LB-MKI67-2M TP[M/V]QKLDL rs7918199 B∗08:01 0.08 Annotated ORF 
LB-PARP4-1A QI[A/T]LHALSL rs2275660 B∗08:01 0.22 Annotated ORF 
LB-PDIA6-1K QTKG[K/R]VKL rs4807 B∗08:01 0.74 Annotated ORF 
LB-RPS14-1K FLA[K/R]KPSAV rs4841 B∗08:01 0.26 Out-of-frame ORF 
LB-RPS4Y1-3 LCKVRKITV Y chromosone B∗08:01 0.50 Annotated ORF 
LB-TAF2-1W EPL[W/R]RGASL rs16893214 B∗08:01 0.20 Upstream ORF 
C∗07:01/C∗07:02 LB-FKBP2-1Q MRLSWF[Q/R]VL rs4672 C∗07:01 0.07 Annotated ORF 
LB-XRCC1-1Q RMRRRLPS[Q/R]RYL rs25487 C∗07:01 0.37 Annotated ORF 
LB-DOCK10-1I VRRV[I/N]QEEI rs78257220 C∗07:02 0.10 Annotated ORF 
Other HLAs LB-MKI67-3E ES[E/K]SVQRVTR rs8473 A∗68:01 0.52 Annotated ORF 
LB-PLK4-1E DSNYPTR[E/D]R rs17012739 A∗68:01 0.32 Annotated ORF 
LB-SRGN-1R ESSVQGYPT[R/Q]R rs2229498 A∗68:01 0.15 Annotated ORF 
LB-PARP4-2A D[A/G]LGVLPAF rs1050110 B∗35:01 0.42 Annotated ORF 
LB-MCM3-1K [K/E]EPFSSVEI rs2230240 B∗40:01 0.29 Annotated ORF 
LB-ARF6-2E S[E/Q]GPGGGGDW rs112017635 B∗44:02 0.14 Upstream ORF 
LB-RAI1-1T AEQGAQV[T/P]F rs11649804 B∗44:02 0.33 Annotated ORF 
LB-HLA-DPA1-2R EEFG[R/Q]AFSF rs1042178 B∗44:02 0.19 Annotated ORF 
LB-ARF6-1E S[E/Q]GPGGGGDW rs112017635 B∗44:03 0.14 Upstream ORF 
LB-HLA-DPA1-1R EEFG[R/Q]AFSF rs1042178 B∗44:03 0.19 Annotated ORF 
LB-INCENP-1D EE[D/E]ARRLRW rs7129085 B∗44:03 0.63 Annotated ORF 
LB-DHX33-2C YLYEGGIS[C/R] rs8069315 C∗03:03 0.12 Annotated ORF 
LB-MYO1G-2M VS[M/V]NPYQEL rs61739531 C∗03:03 0.23 Annotated ORF 
LB-DHX33-3C YLYEGGIS[C/R] rs8069315 C∗03:04 0.12 Annotated ORF 
LB-MYO1G-3M VS[M/V]NPYQEL rs61739531 C∗03:04 0.23 Annotated ORF 
HLAMiHASequence∗ SNPHLA-alleleEuropean population allele frequency† Type of transcript encoding MiHA
Common HLAs 
A∗01:01 LB-LINC01857-1D ST[D/N]ESVLSDY rs1055228 A∗01:01 0.43 lncRNA ORF 
LB-OAS1-1R ETDDPR[R/T]YQKY rs1051042 A∗01:01 0.34 Annotated ORF 
LB-SLC35B1-1H RVD[H/R]TRSWLY rs1135034 A∗01:01 0.09 Annotated ORF 
LB-UAP1L1-1A R[A/V]SDGSLLY rs7037849 A∗01:01 0.60 Annotated ORF 
A∗02:01 LB-DHX38-1W ALHY[W/S]DWTC rs1050361 A∗02:01 0.40 Out-of-frame ORF 
LB-E2F2-1H ALD[H/Q]LIQSC rs2075995 A∗02:01 0.51 Annotated ORF 
LB-LINC02427-1G FLWLGAPP[G/S]M rs1991229 A∗02:01 0.26 lncRNA ORF 
LB-MIS18BP1-1Q K[Q/E]FPITEAV rs34402741 A∗02:01 0.01 Annotated ORF 
LB-MTHFD1-1Q SIIAD[Q/R]IAL rs2236225 A∗02:01 0.43 Annotated ORF 
LB-NDUFAF1-1H KLL[H/R]GTYFL rs1899 A∗02:01 0.27 Annotated ORF 
LB-SLAMF1-1F GLLSLT[F/L]VL rs2295612 A∗02:01 0.78 Annotated ORF 
LB-SSR1-2L VLFRGGPRG[L/S]LAVA rs10004 A∗02:01 0.75 Annotated ORF 
LB-TIAM2-1C RL[C/R]KVIQEL rs11751128 A∗02:01 0.27 Annotated ORF 
A∗03:01 LB-APOBEC3B-3K QVYF[K/E]PQYH rs2076109 A∗03:01 0.40 Annotated ORF 
LB-APOBEC3H-2R [R/G]IFASRLYY rs139297 A∗03:01 0.46 Annotated ORF 
LB-EXO1-1R [R/H]SWDDKTCQK rs735943 A∗03:01 0.57 Annotated ORF 
LB-F13A1-1L ITFYTGV[L/P]K rs5982 A∗03:01 0.21 Annotated ORF 
LB-KLHDC9-1R RLDP[R/S]ARTY rs11576830 A∗03:01 0.34 Annotated ORF 
LB-MCM10-1R RA[R/K]GQVLTK rs2274110 A∗03:01 0.19 Annotated ORF 
LB-NANS-1D KAL[D/E]RPYTSK rs1058446 A∗03:01 0.22 Annotated ORF 
LB-SLC5A6-1F SL[F/L]PLSCQK rs61737373 A∗03:01 0.07 Annotated ORF 
B∗07:02 LB-APOBEC3B-4L TPC[L/P]DCVAKL rs2076110 B∗07:02 0.06 Annotated ORF 
LB-APOBEC3H-1K KPQQ[K/D]GLRLL rs139298, rs139299 B∗07:02 0.52 Annotated ORF 
LB-CYTOR-1W RPLHL[W/R]VVCL rs7657 B∗07:02 0.45 lncRNA ORF 
LB-DDX20-1R TPVDD[R/S]ISL rs197414 B∗07:02 0.87 Annotated ORF 
LB-DHX37-1R KLASY[R/Q]SCL rs4447263 B∗07:02 0.40 Annotated ORF 
LB-DOK2-1L LPRPDSPYSR[L/P] rs34215892 B∗07:02 0.03 Annotated ORF 
LB-ERGIC1-1R [R/G]PWPPTLLL rs477748 B∗07:02 0.29 Alternative transcript 
LB-FANCA-1S VP[S/G]KYRSLL rs2239359 B∗07:02 0.41 Annotated ORF 
LB-FBXO7-1E RPP[E/G]GSGPLL rs9621461 B∗07:02 0.09 Out-of-frame ORF 
LB-HNRNPUL1-1R LPSNSR[R/H]HSSL rs1056854 B∗07:02 0.17 Out-of-frame ORF 
LB-IGSF3-1R SP[R/Q]DTGNYSC rs6703791 B∗07:02 0.17 Annotated ORF 
LB-IL10RA-1R GPRWPP[R/Q]MTH rs2256111 B∗07:02 0.51 Out-of-frame ORF 
LB-KIAA0040-1L HPFE[L/P]RTCL rs1057239 B∗07:02 0.44 Upstream ORF 
LB-LGALS3-1H KPFKI[H/Q]VL rs11125 B∗07:02 0.08 Annotated ORF 
LB-LILRB4-1G [G/D]PRPSPTRSV rs731170 B∗07:02 0.70 Annotated ORF 
LB-LTA-1R RV[R/C]GTTLHLLL rs2229094 B∗07:02 0.29 Annotated ORF 
LB-MKI67-1Q [Q/R]PRAPRESA rs10764749 B∗07:02 0.27 Annotated ORF 
LB-MRPS34-1I RPRDSQ[I/L]YA rs11552431 B∗07:02 0.13 Annotated ORF 
LB-MYO3B-1R AP[R/H]SGWPLRSL rs2161916 B∗07:02 0.44 Out-of-frame ORF 
LB-NUP210-1A [A/V]PVYTSPQL rs6795271 B∗07:02 0.68 Annotated ORF 
LB-PDCD11-2L GPDSSKT[L/F]LCL rs2986014 B∗07:02 0.58 Annotated ORF 
LB-PFAS-1P A[P/S]GHTRRKL rs9891699 B∗07:02 0.17 Annotated ORF 
LB-PPP6R1-1P MPWV[P/L]MSPF rs3745920 B∗07:02 0.34 Out-of-frame ORF 
LB-RPS6KB2-1V SPR[V/A]PVSPLKF rs13859 B∗07:02 0.42 Annotated ORF 
LB-SIK1-1A [A/V]PASRASRGGL rs430554 B∗07:02 0.12 Annotated ORF 
LB-SRP14-1 LPMGRRRSALW rs1059395 B∗07:02 0.18 Out-of-frame ORF 
LB-TXNDC11-1P R[P/L]RGLRLPQL rs3743588 B∗07:02 0.74 Out-of-frame ORF 
LB-TYMSOS-1G RPLP[G/R]RIEV rs2853533 B∗07:02 0.15 lncRNA ORF 
LB-UBE2G2-1R [R/G]PRVAGGLSVC rs7364120 B∗07:02 0.29 Alternative transcript 
LB-USP15-1I MPSHLRN[I/T]LL rs11174420 B∗07:02 0.31 Out-of-frame ORF 
LB-USP15-2T MPSHLRN[T/I]LLM rs11174420 B∗07:02 0.69 Out-of-frame ORF 
LB-ZNF419-2G IPR[G/D]SWWVEL rs2074071 B∗07:02 0.69 Annotated ORF 
B∗08:01 LB-AP3B1-1V VPN[V/E]KSGAL rs6453373 B∗08:01 0.07 Annotated ORF 
LB-ARHGEF39-1R SFP[R/H]EKLLLM rs2297879 B∗08:01 0.33 Annotated ORF 
LB-C12ORF57-1A L[A/V]FYRKAPL rs7965269 B∗08:01 0.70 Upstream ORF 
LB-DEPDC1-1R HLFE[R/Q]ECL rs78030459 B∗08:01 0.05 Out-of-frame ORF 
LB-MKI67-2M TP[M/V]QKLDL rs7918199 B∗08:01 0.08 Annotated ORF 
LB-PARP4-1A QI[A/T]LHALSL rs2275660 B∗08:01 0.22 Annotated ORF 
LB-PDIA6-1K QTKG[K/R]VKL rs4807 B∗08:01 0.74 Annotated ORF 
LB-RPS14-1K FLA[K/R]KPSAV rs4841 B∗08:01 0.26 Out-of-frame ORF 
LB-RPS4Y1-3 LCKVRKITV Y chromosone B∗08:01 0.50 Annotated ORF 
LB-TAF2-1W EPL[W/R]RGASL rs16893214 B∗08:01 0.20 Upstream ORF 
C∗07:01/C∗07:02 LB-FKBP2-1Q MRLSWF[Q/R]VL rs4672 C∗07:01 0.07 Annotated ORF 
LB-XRCC1-1Q RMRRRLPS[Q/R]RYL rs25487 C∗07:01 0.37 Annotated ORF 
LB-DOCK10-1I VRRV[I/N]QEEI rs78257220 C∗07:02 0.10 Annotated ORF 
Other HLAs LB-MKI67-3E ES[E/K]SVQRVTR rs8473 A∗68:01 0.52 Annotated ORF 
LB-PLK4-1E DSNYPTR[E/D]R rs17012739 A∗68:01 0.32 Annotated ORF 
LB-SRGN-1R ESSVQGYPT[R/Q]R rs2229498 A∗68:01 0.15 Annotated ORF 
LB-PARP4-2A D[A/G]LGVLPAF rs1050110 B∗35:01 0.42 Annotated ORF 
LB-MCM3-1K [K/E]EPFSSVEI rs2230240 B∗40:01 0.29 Annotated ORF 
LB-ARF6-2E S[E/Q]GPGGGGDW rs112017635 B∗44:02 0.14 Upstream ORF 
LB-RAI1-1T AEQGAQV[T/P]F rs11649804 B∗44:02 0.33 Annotated ORF 
LB-HLA-DPA1-2R EEFG[R/Q]AFSF rs1042178 B∗44:02 0.19 Annotated ORF 
LB-ARF6-1E S[E/Q]GPGGGGDW rs112017635 B∗44:03 0.14 Upstream ORF 
LB-HLA-DPA1-1R EEFG[R/Q]AFSF rs1042178 B∗44:03 0.19 Annotated ORF 
LB-INCENP-1D EE[D/E]ARRLRW rs7129085 B∗44:03 0.63 Annotated ORF 
LB-DHX33-2C YLYEGGIS[C/R] rs8069315 C∗03:03 0.12 Annotated ORF 
LB-MYO1G-2M VS[M/V]NPYQEL rs61739531 C∗03:03 0.23 Annotated ORF 
LB-DHX33-3C YLYEGGIS[C/R] rs8069315 C∗03:04 0.12 Annotated ORF 
LB-MYO1G-3M VS[M/V]NPYQEL rs61739531 C∗03:04 0.23 Annotated ORF 
∗

Polymorphic AAs are shown between brackets. Bold AA is present in the MiHA, whereas the other AA is present in the allelic variant.

†

Allele frequency of the MiHA-encoding SNP as reported in the 1000 Genomes Project for the European population.

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