St. Jude Research

SAMD9 Mutations

View SAMD9L Mutations

The SAMD9 Database is a curated repository of germline SAMD9 variants identified in patients through published literature and direct referrals. Our goal is to provide a comprehensive knowledge base for understanding SAMD9/9L syndromes.

If you are interested in contributing variants, please contact wlodarskilab@stjude.org

SAMD9 transcript version is NM_017654.3. Curated by Sushree Sahoo, PhD. Last updated: 07/29/2025.

Patient ID SAMD9 mutation (cDNA) SAMD9 mutation (Protein) Type of mutation Zygosity Inheritance CADD score Mutation effect (HEK293 assay) gnomAD (v4.1.0) population frequency Year of reporting PMID Patient also reported in (PMID) Original patient ID Disease Karyotype Constitutional abnormalities Hematopoietic phenotype Infections Somatic SAMD9 mutations Other somatic mutations
P001 c.3839C>T p.Pro1280Leu Missense Heterozygous 16.18   Absent 2016 27182967   P8 (Family7) MIRAGE Normal Yes Yes      
P002 c.3584C>T p.Ala1195Val Missense Heterozygous 24.8 Growth inhibited Absent 2016 27182967   P7 (Family6) MIRAGE   Yes Yes Yes    
P003 c.2305G>A p.Asp769Asn Missense Heterozygous 24.1 Growth inhibited Absent 2016 27182967   P3 (Family3) MIRAGE Normal Yes Yes Yes    
P004 c.2305G>A p.Asp769Asn Missense Heterozygous 24.1 Growth inhibited Absent 2016 27182967 29365320 P4 (Family3) MIRAGE Monosomy 7, trisomy 21 Yes Yes Yes    
P005 c.2920G>A p.Glu974Lys Missense Heterozygous 24.4 Growth inhibited Absent 2016 27182967   P6 (Family5) MIRAGE   Yes Yes Yes    
P006 c.2500A>T p.Asn834Tyr Missense Heterozygous 26.3 Growth inhibited Absent 2016 27182967   P5 (Family4) MIRAGE   Yes Yes Yes    
P007 c.3856C>A p.Gln1286Lys Missense Heterozygous 18.61 Growth inhibited Absent 2016 27182967   P9 (Family8) MIRAGE   Yes Yes Yes    
P008 c.3877C>T p.Arg1293Trp Missense Heterozygous 16.21 Growth inhibited Absent 2016 27182967   P10 (Family9) MIRAGE Normal Yes Yes Yes    
P009 c.3877C>T p.Arg1293Trp Missense Heterozygous 16.21 Growth inhibited Absent 2016 27182967   P11 (Family10) MIRAGE Monosomy 7 Yes Yes Yes    
P010 c.1376G>A p.Arg459Gln Missense Heterozygous 18.54 Growth inhibited Absent 2016 27182967   P1 (Family1) MIRAGE   Yes Yes Yes    
P011 c.1376G>A p.Arg459Gln Missense Heterozygous 18.54 Growth inhibited Absent 2016 27182967   P2 (Family2) MIRAGE   Yes Yes Yes    
P012 c.2333C>T p.Thr778Ile Missense     11.85 Growth inhibited Absent 2017 29146900   P4 (SJ018211)* MDS Monosomy 7, 45,XX,del(5)(q31q33) Yes     RIT, ETV6, KCTD10, PTPN11, FREM2, ACACA, SETBP1, ALPP, GAD1, FAM123B
P013 c.3406G>C p.Glu1136Gln Missense Heterozygous Maternally inherited 16.08 Growth inhibited Absent 2017 28487541   P1 (Family1) MDS Monosomy 7 Yes Yes   SAMD9 c.661C>T (p.Arg221X) ETV6 
P014 c.3406G>C p.Glu1136Gln Missense Heterozygous Maternally inherited 16.08 Growth inhibited Absent 2017 28487541   P2 (Family1) MDS Monosomy 7   Yes   SAMD9 c.1747C>A (p.Phe583Ile)
P015 c.3406G>C p.Glu1136Gln Missense Heterozygous Maternally inherited 16.08 Growth inhibited Absent 2017 28487541   P3 (Family1) MDS Monosomy 7, UPD7q Yes     RAD21 
P016 c.3878G>A p.Arg1293Gln Missense Heterozygous 13.86 Growth inhibited Absent 2017 28346228   P1 MIRAGE Normal Yes     No  
P017 c.2471G>A p.Arg824Gln Missense Heterozygous De novo 17.32 Growth inhibited Absent 2017 29266745   P1 MIRAGE Monosomy 7 Yes Yes Yes    
P018 c.2948T>G p.Ile983Ser Missense Heterozygous 24.7 Growth inhibited Absent 2017 28346228 29365320, 34621053 P8 MIRAGE Normal, progressed to Monosomy 7 Yes Yes Yes SAMD9 c.2294delA (p.Asn765ThrfsX13, cis to germline SAMD9)
P019 c.4707G>T p.Lys1569Asn Missense Heterozygous 15.15 Growth inhibited Absent 2017 28346228 29365320 P7 MIRAGE Normal, progressed to Monosomy 7 Yes Yes Yes SAMD9 c.1030C>T (p.Arg344X, cis to germline SAMD9)
P020 c.3878G>A p.Arg1293Gln Missense Heterozygous De novo 13.86 Growth inhibited Absent 2017 28346228   P2 MIRAGE   Yes   Yes    
P021 c.1376G>A p.Arg459Gln Missense Heterozygous 18.54 Growth inhibited Absent 2017 28346228   P4 MIRAGE Normal, progressed to Monosomy 7 Yes   Yes No  
P022 c.2054G>A p.Arg685Gln Missense Heterozygous 24.8 Growth inhibited Absent 2017 28346228   P6 MIRAGE Normal, progressed to Monosomy 7 and del(7q) Yes Yes Yes No  
P023 c.2944C>T p.Arg982Cys Missense Heterozygous 20.2 Growth inhibited 0.00039%  2017 28346228   P3 MIRAGE Normal Yes Yes Yes SAMD9 c.79A>T (p.Lys27X, cis to germline SAMD9)
P024 c.2944C>T p.Arg982Cys Missense Heterozygous 20.2 Growth inhibited 0.00039%  2017 28346228   P5 MIRAGE Normal, progressed to Monosomy 7 Yes   Yes SAMD9 c.4597C>T (p.Arg1533X, cis to germline SAMD9)
P025 c.2945G>A p.Arg982His Missense Heterozygous 21.8 Growth inhibited Absent 2017 28346228   P2 MIRAGE Normal Yes Yes Yes No  
P026 c.2026A>G p.Lys676Glu Missense Heterozygous 16.18 Growth inhibited Absent 2018 30046003   2B (Family2, sibling of 2A) MDS-related AML Monosomy 7   Yes     ETV6 
P027 c.2947A>G p.Ile983Val Missense Heterozygous De novo 16.93   Absent 2018 29146883   P6 (UB026) Aplastic anemia Isolated Monosomy 7 Yes Yes      
P028 c.3558_3562del p.Lys1186fs Frameshift Heterozygous Maternally inherited   Absent 2018 29146883   P3 (UB037) RCMD Normal Yes Yes      
P029 c.2326C>A p.Gln776Lys Missense     24.9   Absent 2018 29146883   P5 (UB062) MIRAGE with aplastic anemia Monosomy 7 Yes Yes   SAMD9 c.2045A>G (p.Glu682Gly)
P030 c.2182A>G p.Thr728Ala Missense     0.049   Absent 2018 29146883   P4 (UB660) RCMD Transient monosomy7 Yes Yes      
P031 c.1406A>C p.Tyr469Cys Missense Heterozygous De novo 18.8   Absent 2018 29146883   P2 (UB136) RCMD Monosomy 7 Yes Yes      
P032 c.1406A>G p.Tyr469Ser Missense     14.73   Absent 2018 29146883   P1 (UB096) Aplastic anemia Monosomy 7 Yes Yes      
P033 c.1922T>C p.Leu641Pro Missense     25.5   Absent 2018 30565860   P1 MIRAGE Monosomy 7, UPD7q Yes Yes Yes    
P034 c.3049T>G p.Phe1017Val Missense Heterozygous De novo 17.9 Growth inhibited Absent 2018 30403727   P1 MIRAGE Normal Yes Yes Yes    
P035 c.2026A>G p.Lys676Glu Missense Heterozygous 16.18 Growth inhibited Absent 2018 30046003   2A (Family2, proband) MDS-related AML Monosomy 7     Yes   del12p13.2(ETV6), SETBP1, ASXL1
P036 c.2944C>T p.Arg982Cys  Missense     20.2 Growth inhibited 0.00039%  2018 29506479   P1 MIRAGE Normal Yes Yes Yes    
P037 c.2920G>A p.Glu974Lys Missense     24.4 Growth inhibited Absent 2018 29365320   P2 MIRAGE Monosomy 7, del(7q) Yes Yes Yes    
P038 c.2462A>T p.Lys821Met Missense Heterozygous De novo 22.8 Growth inhibited Absent 2018 29365320   P1 MIRAGE Normal Yes Yes Yes    
P039 c.2165C>A p.Ala722Glu Missense Heterozygous De novo 15.43   Absent 2018 29175836   P1 MIRAGE Normal Yes Yes Yes SAMD9 c.2053C>T (p.Arg695X)
P040 c.2306A>G p.Asp769Gly Missense Heterozygous De novo 24.7   Absent 2018 29175836   P2 MIRAGE Normal Yes No Yes SAMD9 c.115C>T (p.Gln39X)
P041 c.2691A>G p.Ile897Met Missense Heterozygous 21.7 Growth inhibited Absent 2018 28834235 19760774, 29365320 P1 MIRAGE Monosomy 7 Yes Yes Yes    
P042 c.2333C>T p.Thr778Ile Missense     11.85 Growth inhibited Absent 2019 31572304   P2 (Family1, mother of P1) MIRAGE   Yes Yes   SAMD9 c.661C>T (p.Arg221X)
P043 c.1376G>A p.Arg459Gln Missense Heterozygous 18.54 Growth inhibited Absent 2019 31666768   P1 MIRAGE   Yes Yes Yes    
P044 c.2920G>A p.Glu974Lys  Missense Heterozygous De novo 24.4 Growth inhibited Absent 2019 31638924   P1 MIRAGE with coexisting TRMA Yes Yes Yes    
P045 c.2471G>A p.Arg824Gln Missense Heterozygous De novo 17.32 Growth inhibited Absent 2019 31620126   P1 MIRAGE without adrenal hypoplasia Normal, progressed to Monosomy 7 Yes Yes Yes    
P046 c.2333C>T p.Thr778Ile Missense Heterozygous Maternally inherited 11.85 Growth inhibited Absent 2019 31572304   P1 (Family1) MIRAGE Normal Yes Yes Yes SAMD9 c.853C>T (p.Arg285X)
P047 c.2407G>C p.Glu803Gln Missense Heterozygous De novo 23.5   Absent 2019 31306780   P5 MIRAGE Monosomy 7 Yes Yes Yes    
P048 c.4690G>A p.Gly1564Ser Missense Heterozygous 27.3   Absent 2019 31306780   P2 MIRAGE Monosomy 7, del7q13, UPD7q Yes Yes Yes    
P049 c.2318T>C p.Ile773Thr Missense Heterozygous 25   Absent 2019 30900330 31306780 P1 MIRAGE   Yes Yes Yes    
P050 c.1447C>G p.Leu483Val Missense Heterozygous 23.1   Absent 2020 31900929   P1(II-1) MDS   Yes Yes      
P051 c.1447C>G p.Leu483Val Missense Heterozygous Maternally inherited 23.1   Absent 2020 31900929   P2(III-1) MDS del(7q) Yes Yes   c.2958C> G (p.Ser986Cis) ZRSR2
P052 c.1447C>G p.Leu483Val Missense Heterozygous Maternally inherited 23.1   Absent 2020 31900929   P3(IV-1) MDS   Yes Yes      
P053 c.689G>A p.Arg230His Missense Heterozygous 24.2   0.01% 2020 32594144   P1 Tumoral cutaneous calcifications with coexisting Trisomy 21 Yes Yes      
P054 c.1927A>G p.Lys643Glu Missense Heterozygous 17.36 Growth inhibited Absent 2020 32770553   P22 MDS-LB Monosomy 7 No Yes Yes    
P055 c.4615T>A p.Leu1539Ile Missense     4.177   Absent 2020 32787808   P1 MIRAGE with nephrotic syndrome Normal Yes Yes Yes    
P056 c.3221G>T p.Ser1074Ile Missense Heterozygous 16.28   Absent 2020 32619790   P1 MIRAGE Monosomy 7 Yes Yes Yes   ETV6, SETBP1,  RUNX1
P057 c.4435G>T p.Ala1479Ser Missense Heterozygous De novo 20.1   Absent 2020 32194975 34629738 P1 MIRAGE Normal Yes Yes Yes    
P058 c.2462A>T p.Lys821Met Missense     22.8 Growth inhibited Absent 2020 32106287   P2 MIRAGE   Yes Yes Yes    
P059 c.3878G>A p.Arg1293Gln  Missense Heterozygous De novo 13.86 Growth inhibited Absent 2020 32106287   P1 MIRAGE   Yes Yes Yes    
P060 c.2920G>A p.Glu974Lys Missense Heterozygous 24.4 Growth inhibited Absent 2020 31208161   P1 MIRAGE Monosomy 7 Yes Yes Yes    
P061 c.3274T>C p.Phe1092Leu Missense Heterozygous 23.5 Growth inhibited Absent 2021 34621053   A083 MDS-LB Monosomy 7 No Yes No   No
P062 c.2300C>T p.Thr767Ile Missense Heterozygous 23.7 Growth inhibited Absent 2021 34621053   CH016 MDS-LB Normal No Yes No   ASXL1
P063 c.448A>T p.Thr150Ser Missense Heterozygous 0.002 Growth inhibited Absent 2021 34621053   D1115 MDS-LB Monosomy 7 No Yes No   No
P064 c.2629A>G p.Lys877Glu Missense Heterozygous 7.637 Growth inhibited Absent 2021 34621053   D1142 MDS-LB Monosomy 7 Yes Yes No   No
P065 c.98G>A p.Arg33Lys Missense Heterozygous 20.7 Growth inhibited Absent 2021 34621053   D1164 MDS-LB Normal No Yes No   No
P066 c.4334_4336del p.Gln1445del Missense Heterozygous 13.63 Growth inhibited 0.00% 2021 34621053   D1266 MDS-LB Normal No Yes No   No
P067 c.3878G>A p.Arg1293Gln Missense Heterozygous 22.7 Growth inhibited Absent 2021 34621053   D1320 MIRAGE Monosomy 7 Yes Yes No   SETBP1
P068 c.401G>C p.Gly134Ala Missense Heterozygous 0.001 Growth inhibited Absent 2021 34621053   D424 MDS-LB Normal Yes Yes No   ASXL1
P069 c.1326delT p.Phe442LeufsX19 Frameshift Heterozygous 25.4   0.00% 2021 34621053   D430 MDS-LB Normal No Yes No   No
P070 c.3826G>A p.Val1276Ile Missense Heterozygous 14.12 Growth inhibited Absent 2021 34621053   D534 MDS-EB Monosomy 7 Yes Yes No   SETBP1
P071 c.2134G>A p.Glu712Lys Missense Heterozygous 18.91   Absent 2021 34621053   D554 MDS-LB Normal Yes Yes No   No
P072 c.731A>G p.His244Arg Missense Heterozygous 23.6 Growth inhibited 0.01% 2021 34621053   D628 MDS-EB Normal No Yes No   No
P073 c.3986T>A p.Val1329Glu Missense Heterozygous 1.862 Growth inhibited Absent 2021 34621053   D640 MDS-EB Normal No Yes No   No
P074 c.1395T>G p.Phe465Leu Missense Heterozygous 0.415 No growth inhibition Absent 2021 34621053   D662 MDS-LB Normal Yes Yes No   No
P075 c.2066T>C p.Val689A Missense Heterozygous 14.98   Absent 2021 34621053   D732 MDS-LB Normal Yes Yes No   No
P076 c.4586G>A p.Arg1529His Missense Heterozygous 25.6 Growth inhibited 0.01% 2021 34621053   D791 MDS-LB Normal Yes Yes No   No
P077 c.2122A>G p.Arg708Gly Missense Heterozygous 24.3 Growth inhibited Absent 2021 34621053   D813 MDS-LB Normal No Yes No   No
P078 c.740T>C p.Ile247Thr Missense Heterozygous 23.8   0.01% 2021 34621053   D831 MIRAGE Normal Yes Yes No   No
P079 c.662G>A p.Arg221Gln Missense Heterozygous 23.5 Growth inhibited 0.01% 2021 34621053   D877 MDS-LB Normal Yes Yes No   No
P080 c.2920G>A p.Glu974Lys Missense Heterozygous 25.6 Growth inhibited Absent 2021 34621053   D977 MDS-LB Normal Yes Yes No   No
P081 c.4701A>G p.Ile1567Met Missense Heterozygous 24.6 Growth inhibited Absent 2021 34621053   E038 MDS-LB Monosomy 7 No Yes No   No
P082 c.4433T>C p.Ile1478Thr Missense Heterozygous 19.57   Absent 2021 34621053   E084 MDS-LB Normal No Yes No   No
P083 c.2964T>G p.Ile988Met Missense Heterozygous 19.22 Growth inhibited Absent 2021 34621053   GR001 MDS-LB Monosomy 7 Yes Yes No   ETV6 
P084 c.731A>G p.His244Arg Missense Heterozygous 23.6 Growth inhibited 0.01% 2021 34621053   GR010 MDS-LB Monosomy 7 Yes Yes No   No
P085 c.2248A>T p.Ile750Phe Missense Heterozygous 23.7 Growth inhibited Absent 2021 34621053   I336 MIRAGE Monosomy 7 Yes Yes No   No
P086 c.3570T>G p.Asp1190Glu Missense Heterozygous 0.002 Growth inhibited Absent 2021 34621053   I363 MDS-LB Monosomy 7 No Yes No   No
P087 c.2704C>T p.Arg902Trp Missense Heterozygous 26.1 Growth inhibited 0.00% 2021 34621053   PL082 MDS-EB Monosomy 7 No Yes No   No
P088 c.3040G>A p.Glu1014Lys Missense Heterozygous 23 Growth inhibited Absent 2021 34621053   D1177 MDS-LB Monosomy 7 Yes Yes Yes   No
P089 c.4364_4365del p.Glu1455ValfsX14 Frameshift Heterozygous 23.9 Growth inhibited Absent 2021 34621053   D1248 MDS-LB Monosomy 7, UPD7q No Yes Yes   EZH2
P090 c.2945G>A p.Arg982His Missense     21.8 Growth inhibited Absent 2021 34621053   P1 MIRAGE   Yes Yes     No
P091 c.1923_1925del p.Leu642del Missense Heterozygous 1.807 Growth inhibited Absent 2021 34621053   D130 MDS-LB Monosomy 7 Yes Yes Yes   SETBP1,  ASXL1, PTPN11
P092 c.2854G>C p.Gly952Arg Missense Heterozygous 5.36 Growth inhibited 0.04% 2021 34621053   D484 MDS-LB Normal Yes Yes Yes   No
P093 c.4541G>A p.Ser1514Asn Missense Heterozygous 18.217 Growth inhibited Absent 2021 34621053   D641 MDS-LB Monosomy 7 Yes Yes Yes   RUNX1, PTPN11, CBL
P094 c.2319T>G p.Ile773Met Missense Heterozygous 23.2 Growth inhibited Absent 2021 34621053   D676 MDS-LB Monosomy 7 No Yes Yes   No
P095 c.3563G>C p.Arg1188Pro Missense Heterozygous 23.7 Growth inhibited Absent 2021 34621053   D769 MIRAGE Monosomy 7 Yes Yes Yes   No
P096 c.1395T>G p.Phe465Leu Missense Heterozygous 0.415 No growth inhibition Absent 2021 34621053   D778 MDS-LB Monosomy 7 No Yes Yes   ASXL1, SETBP1, MYB
P097 c.2770C>G p.Leu924Val Missense Heterozygous 23.9 Growth inhibited Absent 2021 34621053   D893 MDS-LB Monosomy 7 Yes Yes Yes   EZH2, RUNX1
P098 c.2065G>T p.Val689Leu Missense Heterozygous 26.6   Absent 2021 34621053   D971 MDS-LB Complex Yes Yes Yes   No
P099 c.2627A>G p.His876Arg Missense Heterozygous 23.3   Absent 2021 34621053   GR015 MDS-LB Normal Yes Yes Yes   No
P100 c.1310T>C p.Phe437Ser Missense Heterozygous De novo 25.9 Growth inhibited Absent 2021 34253717   P1 MIRAGE with familial dysautonomia Monosomy 7 Yes Yes Yes    
P101 c.3878G>A p.Arg1293Gln Missense Heterozygous De novo 13.86 Growth inhibited Absent 2021 33427306   P1 MIRAGE with achalasia Yes   Yes    
P102 c.3406G>C p.Glu1136Gln Missense Heterozygous De novo 16.08 Growth inhibited Absent 2021 34659124   P1 MIRAGE Normal Yes Yes Yes    
P103 c.3821A>G p.Tyr1274Cys Missense Heterozygous De novo 24.1   Absent 2021 32054657   P4 (23) BMF Monosomy 7 Yes Yes      
P104 c.2318T>C p.Ile773Thr Missense Heterozygous De novo 25   Absent 2021 32054657   P3 (62) BMF Monosomy 7 Yes Yes Yes    
P105 c.4057A>G p.Lys1353Glu Missense Heterozygous De novo 13.83   Absent 2021 32054657   P2 (20) BMF Transient Monosomy7 Yes Yes Yes    
P106 c.2471G>A p.Arg824Gln Missense Heterozygous De novo 17.32 Growth inhibited Absent 2022 35707773   P1 COVID-19-MIS No No No    
P107 c.3877C>T p.Arg1293Trp Missense Heterozygous 16.21 Growth inhibited Absent 2022 35994417   P1 MIRAGE   Yes No Yes    
P108 c.4460A>G p.Lys1487Arg Missense Heterozygous Maternally inherited 8.216   0.00% 2023 37160314   P1 MDS-EB Monosomy 7, inversion chr 3 No Yes No   KRAS, MPL, KMT2C, SF3B1
P109 NA p.Gln1198His Missense Heterozygous De novo     Absent 2023 37357006   P5 BMF Normal Yes Yes Yes   No
P110 c.4598G>A p.Arg1533Gln Missense Heterozygous De novo 17.88   Absent 2023 37586839   P1 MIRAGE Normal Yes       No
P111 c.3070A>G p.Lys1024Glu Missense Heterozygous 22.5   Absent 2023 37195360   P1 MIRAGE   Yes Yes Yes    
P112 c.2945G>A p.Arg982His Missense Heterozygous 21.8 Growth inhibited Absent 2023 37044079   P1 MIRAGE with severe temperature instability Yes No Yes    
P113 c.2471G>A p.Arg824Gln Missense Heterozygous De novo 17.32 Growth inhibited Absent 2023 36730951   P1 MDS Monosomy 7 Yes Yes Yes    
P114 c.2944C>T p.Arg982Cys  Missense Heterozygous De novo 20.2   0.00% 2024 38213203   P1 MIRAGE   Yes Yes Yes    
P115 c.1972A>G p.Asn658Asp Missense Heterozygous 24.4   Absent 2024 39348076   P1 MIRAGE Normal Yes Yes Yes   No
P116 c.2159del p.Asn720ThrfsX35 Frameshift Heterozygous     Absent 2024 38529548   P1 MIRAGE with dysautonomia Transient Monosomy7 Yes Yes Yes    
P117 c.480_481del p.Val162IlefsX5 Frameshift Homozygous       Absent 2024 37830462   P1 MIRAGE (GI defects and developmental delay) Normal Yes No No   No
P118 c.1800_1801delAA p.Glu600AspfsX12  Frameshift Heterozygous     Absent 2025 40725152   P14 MDS            

Abbreviations:
AML: acute myeloid leukemia, BMF: bone marrow failure, COVID19-MIS: COVID19-associated multisystem inflammatory syndrome, MDS: myelodysplastic syndrome, MDS-EB: MDS with excess blast, MDS-LB: MDS with low blast, MIRAGE: myelodysplasia, infection, restriction of growth, adrenal hypoplasia, genital anomalies, enteropathy, RCMD: refractory cytopenia with multilineage dysplasia, TRMA: thiamine-responsive megaloblastic anemia, UPD: uniparental isodisomy