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Resources for Genetics Professionals — Genetic Disorders Associated with Founder Variants Common in the Ashkenazi Jewish Population

, MD and , PhD.

Author Information and Affiliations

Initial Posting: ; Last Revision: October 20, 2022.

Estimated reading time: 13 minutes

A founder variant is a pathogenic variant observed at high frequency in a specific population due to the presence of the variant in a single ancestor or small number of ancestors. The presence of a founder variant can affect the approach to molecular genetic testing. When one or more founder variants account for a large percentage of all pathogenic variants found in a population, testing for the founder variant(s) may be performed first.

The table below includes common founder variants – here defined as three or fewer variants that account for >50% of the pathogenic variants identified in a single gene in individuals of a specific ancestry – in individuals of Ashkenazi Jewish ancestry. Note: (1) Pathogenic variants that are common worldwide due to a DNA sequence hot spot are not considered founder variants and thus are not included. (2) Disorders with a carrier frequency ≤1/200 are not included.

Table.

Genetic Disorders Associated with Founder Variants Common in the Ashkenazi Jewish Population

GeneDisorderMOIDNA Nucleotide
Change
Predicted
Protein
Change
Proportion
of Pathogenic
Variants in
Gene 1
Carrier FrequencyReference
Sequences
References 2
ABCC8 Familial hyperinsulinism ARc.3989-9G>A--93%1/83 NM_000352​.6 Zlotogora et al [2018]
ACADS Short chain acyl-CoA dehydrogenase deficiency ARc.319C>Tp.Arg107Cys70%1/15 to 1/26 NM_000017​.4
NP_000008​.1
Tein et al [2008], Zlotogora et al [2018]
ACSF3 Combined malonic & methylmalonic aciduria (OMIM 614265)ARc.1411C>Tp.Arg471Trp~100% 31/69 NM_174917​.5
NP_777577​.2
Zlotogora et al [2018]
ADAMTS2 Ehlers-Danlos syndrome, dermatosparaxis type (OMIM 225410)ARc.673C>Tp.Gln225Ter95%1/159 to 1/187 NM_014244​.5
NP_055059​.2
Shi et al [2017], Zlotogora et al [2018]
APC Colorectal cancer (See APC-Associated Polyposis Conditions.)ADc.3920T>Ap.Ile1307Lys92%NA NM_000038​.6
NP_000029​.2
Ukaegbu et al [2021]
ASPA Canavan disease ARc.854A>Cp.Glu285Ala83%1/55 NM_000049​.4
NP_000040​.1
Kaul et al [1994], Lazarin et al [2013], Zlotogora et al [2018]
c.693C>Ap.Tyr231Ter15%
ATP7B Wilson disease ARc.3191A>Cp.Glu1064Ala85%1/67 NM_000053​.4
NP_000044​.2
Shi et al [2017]
c.3207C>Ap.His1069Gln
c.1934T>Gp.Met645Arg
BBS2 Bardet-Biedl syndrome ARc.311A>Cp.Asp104Ala25%1/139 NM_031885​.5
NP_114091​.4
Shi et al [2017], Zlotogora et al [2018]
c.1895G>Cp.Arg632Pro75%
BCKDHB Maple syrup urine disease ARc.548G>Cp.Arg183Pro81%1/97 NM_183050​.4
NP_898871​.1
Zlotogora et al [2018]
c.832G>Ap.Gly278Ser19%
BLM Bloom syndrome ARc.2207_2212delATCTGAinsTAGATTCp.Tyr736LeufsTer598%-99%1/104 to 1/134 NM_000057​.4
NP_000048​.1
German et al [2007], Scott et al [2010], Lazarin et al [2013], Zlotogora et al [2018]
BRCA1 BRCA1- and BRCA2-associated hereditary breast and ovarian cancer ADc.68_69delAGp.Glu23ValfsTer1772%NA NM_007294​.4
NP_009225​.1
Bahar et al [2001], Frank et al [2002], Phelan et al [2002], Ferla et al [2007], Cox et al [2018]
c.5266dupCp.Gln1756ProfsTer7426%
BRCA2 c.5946delTp.Ser1982ArgfsTer2295% NM_000059​.4
NP_000050​.3
CCDC65 Primary ciliary dyskinesia ARc.877_878delATp.Ile293ProfsTer2~100% 31/118 to 1/344 NM_033124​.5
NP_149115​.2
Austin-Tse et al [2013], Horani et al [2013]
CCM2 Cerebral cavernous malformation ADc.30+5_30+6delGCinsTT-->70%NA NM_031443​.4 Gallione et al [2011]
CFTR Cystic fibrosis ARc.3846G>Ap.Trp1282Ter45%-50%1/55 NM_000492​.4
NP_000483​.3
Scott et al [2010], Lazarin et al [2013], Zlotogora et al [2018]
c.1521_1523delCTTp.Phe508del27%-34%1/88
c.3454G>Cp.Asp1152His7%-14%1/175
CHEK2 Hereditary breast and ovarian cancer (OMIM 114480)ADc.1283C>Tp.Ser428Phe67%NA NM_007194​.4
NP_009125​.1
Leedom et al [2016], Nielsen et al [2016], Walsh et al [2017], Cox et al [2018]
c.1100delCp.Thr367MetfsTer1517%
c.470T>Cp.Ile157Thr11%
CHRNE Congenital myasthenic syndrome ARc.1353dupGp.Asn452GlufsTer485%1/182 to 1/200 NM_000080​.4
NP_000071​.1
Zlotogora et al [2018]
CLRN1 Usher syndrome type 3A (OMIM 276902)ARc.144T>Gp.Asn48Lys~100% 31/92 to 1/120 NM_174878​.3
NP_777367​.1
Scott et al [2010], Zlotogora et al [2018]
CNGA3 Achromatopsia ARc.1669G>Ap.Gly557Arg<100% 41/169 NM_001298​.3
NP_001289​.1
Zlotogora et al [2018]
COL4A3 Alport syndrome ARc.40_63del24p.Leu14_Leu21del95%1/192 NM_000091​.5
NP_000082​.2
Shi et al [2017], Zlotogora et al [2018]
COQ4 Mitochondrial encephalomyopathy (See Primary Coenzyme Q10 Deficiency.)ARc.718C>Tp.Arg240Cys~100% 31/149 to 1/161 NM_016035​.5
NP_057119​.3
Zlotogora et al [2018]
CPT2 Carnitine palmitoyltransferase II deficiency ARc.338C>Tp.Ser113Leu40%1/51 NM_000098​.3
NP_000089​.1
Shi et al [2017], Zlotogora et al [2018]
c.1239_1240delGAp.Lys414ThrfsTer725%
c.1342T>Cp.Phe448Leu25%
CRB2 Ventriculomegaly w/cystic kidney disease (OMIM 219730)ARc.2400C>Gp.Asn800Lys68%1/66 NM_173689​.7
NP_775960​.4
Zlotogora et al [2018]
c.1928A>Cp.Glu643Ala32%
DCXR Pentosuria (OMIM 260800)ARc.583delCp.His195ThrfsTer780%1/29 NM_016286​.4
NP_057370​.1
DGAT1 Protein-losing enteropathy (OMIM 615863)ARc.751+2T>C--~100% 31/90 NM_012079​.6
DHCR7 Smith-Lemli-Opitz syndrome ARc.964-1G>C--93%1/40 NM_001360​.3 Shi et al [2017], Zlotogora et al [2018]
DHDDS Retinitis pigmentosa, nonsyndromic ARc.124A>Gp.Lys42Glu<100% 41/90 to 1/118 NM_024887​.4
NP_079163​.2
Zelinger et al [2011], Shi et al [2017], Zlotogora et al [2018]
DLD Dihydrolipoamide dehydrogenase deficiency ARc.685G>Tp.Gly229Cys72%1/61 to 1/108 NM_000108​.5
NP_000099​.2
Shaag et al [1999], Scott et al [2010], Zlotogora et al [2018]
c.104dupAp.Tyr35Ter28%
DNAH5 Primary ciliary dyskinesia ARc.7502G>Cp.Arg2501Pro86%1/143 to 1/172 NM_001369​.3
NP_001360​.1
Fedick et al [2015], Baskovich et al [2016], Zlotogora et al [2018]
DNAI2 c.1304G>Ap.Trp435Ter~100% 31/145 to 1/200 NM_023036​.6
NP_075462​.3
Knowles et al [2013], Zlotogora et al [2018]
ELP1 Familial dysautonomia ARc.2204+6T>C-->99%1/31 to 1/43 NM_003640​.5 Scott et al [2010], Lazarin et al [2013]
EYS Retinitis pigmentosa ARc.9286_9295delGTAAATATCGp.Val3096LeufsTer28<100% 41/189 NM_001142800​.2
NP_001136272​.1
Zlotogora et al [2018]
F11 Factor XI deficiency (OMIM 612416)AD
AR
c.403G>Tp.Glu135Ter42%1/12 NM_000128​.4
NP_000119​.1
c.901T>Cp.Phe301Leu57%
FAH Tyrosinemia type 1 ARc.782C>Tp.Pro261Leu>99%1/132 to 1/143 NM_000137​.4
NP_000128​.1
Elpeleg et al [2002], Shi et al [2017], Zlotogora et al [2018]
c.1062+5G>A-- NM_000137​.4
FANCC Fanconi anemia ARc.456+4A>T-->99%1/83 to 1/100 NM_000136​.3 Scott et al [2010], Lazarin et al [2013], Zlotogora et al [2018]
FKTN Fukuyama congenital muscular dystrophy ARc.1167dupAp.Phe390IlefsTer14~100% 31/63 to 1/90 NM_001079802​.2
NP_001073270​.1
Zlotogora et al [2018]
G6PC Glycogen storage disease type 1A ARc.247C>Tp.Arg83Cys~100% 31/64 to 1/75 NM_000151​.4
NP_000142​.2
Scott et al [2010], Zlotogora et al [2018]
GALT Galactosemia ARc.-1039_+789del5573ins129 5
(5458-bp del; whole-gene del)
--80%1/160 NG_009029​.2 Coffee et al [2006], Shi et al [2017]
c.563A>Gp.Gln188Arg<10% NM_000155​.4
NP_000146​.2
c.855G>Tp.Lys285Asn<10%
GBA1 (GBA) Gaucher disease ARc.1226A>Gp.Asn409Ser88%1/15 NM_001005741​.3
NP_001005741​.1
Scott et al [2010], Lazarin et al [2013], Zlotogora et al [2018]
GBE1 Glycogen storage disease type IV ARc.986A>Cp.Tyr329Ser95%1/68 NM_000158​.4
NP_000149​.4
Hussain et al [2012], Zlotogora et al [2018]
GJB2 GJB2-related autosomal recessive nonsyndromic hearing loss ARc.167delTp.Leu56ArgfsTer2658%1/31 NM_004004​.6
NP_003995​.2
Zlotogora et al [2018]
c.109G>Ap.Val37Ile28%1/63
c.35delGp.Gly12ValfsTer213%1/133
GMPPB Muscular dystrophy & epilepsy (See Congenital Myasthenic Syndromes Overview.)ARc.860G>Ap.Arg287Gln<100% 41/112 NM_013334​.4
NP_037466​.3
GREM1 Colorectal cancer (OMIM 601228)AD40-kb dup incl GREM1 upstream region & SCG5 exons 2-5 5--~100% 3NA NG_033791​.1 Jaeger et al [2012]
HEXA Tay-Sachs disease ARc.1274_1277dupTATCp.Tyr427IlefsTer580%-81%1/27 NM_000520​.6
NP_000511​.2
Kaback et al [1993], Scott et al [2010], Lazarin et al [2013], Zlotogora et al [2018]
c.1421+1G>C--9%-15% NM_000520​.6
HIKESHI Leukodystrophy, early-onset spastic paraparesis, acquired microcephaly (OMIM 616881)ARc.160G>Cp.Val54Leu~100% 31/189 to 1/200 NM_016401​.4
NP_057485​.2
Edvardson et al [2016], Zlotogora et al [2018]
HOGA1 Primary hyperoxaluria type 3 ARc.944_946delAGGp.Glu315del66%Unknown NM_138413​.4
NP_612422​.2
Belostotsky et al [2010], Zlotogora et al [2018]
c.107C>Tp.Ala36Val22%
IDH3A Retinitis pigmentosa & pseudocoloboma (OMIM 619007)ARc.938T>Cp.Met313Thr~100% 31/103 NM_005530​.3
NP_005521​.1
Zlotogora et al [2018]
KIFBP Goldberg-Shprintzen syndrome (OMIM 609460)ARc.1516dupAp.Ile506AsnfsTer3~100% 31/196 NM_015634​.4
NP_056449​.1
LCA5 Leber congenital amaurosis ARc.835C>Tp.Gln279Ter~100% 31/100 to 1/222 NM_181714​.4
NP_859065​.2
LDLR Familial hypercholesterolemia ADc.655_657delGGCp.Gly219del35%-100%NA NM_000527​.5
NP_000518​.1
Durst et al [2001]
LOXHD1 Nonsyndromic hearing loss (See Hereditary Hearing Loss and Deafness Overview.)ARc.4714C>Tp.Arg1572Ter~100% 31/167 to 1/180 NM_144612​.7
NP_653213​.6
Edvardson et al [2011], Zlotogora et al [2018]
MAK Retinitis pigmentosa, nonsyndromic ARc.1297_1298ins353 5
(c.1297ins(Alu))
--99%1/90 NG_030040​.1 Kimchi et al [2018]
MCOLN1 Mucolipidosis IV ARc.406-2A>G--78%1/89 to 1/133 NM_020533​.3 Bach et al [2005], Scott et al [2010], Lazarin et al [2013]
c.-1015_789del6434 5
(g.511_6943del; exon 1-7 del)
--22%
MECR MECR-related neurologic disorder ARc.830+2_830+3insTp.Glu303del69%1/97 NM_016011​.4
NP_057095​.4
Zlotogora et al [2018]
c.695G>Ap.Gly232Glu31%
MEFV Familial Mediterranean fever ARc.442G>Cp.Glu148Gln47%-59%1/5 NM_000243​.3
NP_000234​.1
Aksentijevich et al [1999], Zlotogora et al [2018]
c.1105C>Tp.Pro369Ser20%
c.2177T>Cp.Val726Ala18%-41%
c.2084A>Gp.Lys695Arg12%
MPL Congenital amegakaryocytic thrombocytopenia (OMIM 604498)ARc.79+2T>A--95%1/57 to 1/62 NM_005373​.3 Shi et al [2017], Zlotogora et al [2018]
MSH2 Lynch syndrome ADc.1906G>Cp.Ala636Pro74%NA NM_000251​.3
NP_000242​.1
Goldberg et al [2014]
MSH6 c.3984_3987dupGTCAp.Leu1330ValfsTer1266% NM_000179​.3
NP_000170​.1
c.3959_3962delCAAGp.Ala1320GlufsTer633%
MTTP Abetalipoproteinemia ARc.2593G>Tp.Gly865Ter95%1/131 to 1/185 NM_000253​.4
NP_000244​.2
Benayoun et al [2007], Shi et al [2017], Zlotogora et al [2018]
c.2212delTp.Ser738fs
NEB Nemaline myopathy 2 (OMIM 256030)ARc.7431+1919_7536+374del2502 5
(2.5-kb del of exon 55)
p.Arg2478_Asp2512del>95%1/168 NM_001271208​.2
NP_001258137​.2
Scott et al [2010], Zlotogora et al [2018]
c.9619-2A>G-- NM_001271208​.2
NR2E3 Enhanced S-cone syndrome (OMIM 268100)ARc.932G>Ap.Arg311Gln~80%Unknown NM_014249​.4
NP_055064​.1
Zlotogora et al [2018]
OTOF Deafness ARc.5332G>Tp.Val1778Phe~100% 31/78 to 1/106 NM_194248​.3
NP_919224​.1
OPTN Amyotrophic lateral sclerosis AD

AR

c.381_382insAGp.Asp128ArgfsTer22~100% 31/100 NM_021980​.4
NP_068815​.2
Goldstein et al [2016], Zlotogora et al [2018]
PAH Phenylalanine hydroxylase deficiency ARc.898G>Tp.Ala300Ser24%1/18 NM_000277​.3
NP_000268​.1
Zlotogora et al [2018]
c.506G>Ap.Arg169His24%
c.1208C>Tp.Ala403Val18%
PCDH15 Usher syndrome type 1 ARc.733C>Tp.Arg245Ter66%1/147 NM_033056​.4
NP_149045​.3
Scott et al [2010], Zlotogora et al [2018]
c.5557A>Cp.Met1855Leu34%
PEX2 Zellweger spectrum disorder ARc.355C>Tp.Arg119Ter~100% 31/196 to 1/227 NM_000318​.3
NP_000309​.2
Zlotogora et al [2018]
PKHD1 Polycystic kidney disease, autosomal recessive ARc.3761_3762delCCinsGp.Ala1254GlyfsTer4990%1/105 NM_138694​.4
NP_619639​.3
Shi et al [2017]
c.107C>Tp.Thr36Met
PMM2 PMM2-CDG ARc.422G>Ap.Arg141His90%1/61 NM_000303​.3
NP_000294​.1
RTEL1 Dyskeratosis congenita ARc.3791G>A 6p.Arg1264His78%1/165 NM_001283009​.2
NP_001269938​.1
Zlotogora et al [2018]
RTEL1 c.1548G>Tp.Met516Ile22% NM_032957​.5
NP_116575​.3
SACS ARSACS ARc.7140T>Ap.Asn2380Lys<100% 41/141 NM_014363​.6
NP_055178​.3
SAMHD1 Aicardi-Goutières syndrome AR8984-bp del of exon 1 5--75%1/138 NG_017059​.1 Crow et al [2015], Straussberg et al [2015]
SLC1A4 Spastic tetraplegia, thin corpus callosum, & progressive microcephaly (OMIM 616657)ARc.766G>Ap.Glu256Lys~100% 31/108 NM_003038​.5
NP_003029​.2
Zlotogora et al [2018]
SLC3A1 Cystinuria (OMIM 220100)ARc.808C>Tp.Arg270Ter~100% 31/61 NM_000341​.4
NP_000332​.2
SLC26A4 Pendred syndrome ARc.349C>Tp.Leu117Phe~100% 31/98 NM_000441​.2
NP_000432​.1
SLC38A8 Foveal hypoplasia (OMIM 609218)ARc.848A>Cp.Asp283Ala~100% 31/81 NM_001080442​.3
NP_001073911​.1
SMARCAL1 Schimke immunoosseous dysplasia ARc.863-2A>G--~100% 31/189 NM_014140​.4
SMPD1 Acid sphingomyelinase deficiency ARc.1493G>Tp.Arg498Leu54%-55%1/95 to 1/116 NM_000543​.5
NP_000534​.3
Scott et al [2010], Lazarin et al [2013], Zlotogora et al [2018]
c.996delCp.Phe333SerfsTer5229%
SPATA16 Spermatogenic failure (OMIM 102530)ARc.848G>Ap.Arg283Gly~100% 31/196 NM_031955​.6
NP_114161​.3
Zlotogora et al [2018]
STRC Deafness ARc.4171C>Gp.Arg1391Gly~100% 31/200 NM_153700​.2
NP_714544​.1
TECPR2 Hereditary sensory & autonomic neuropathy w/intellectual disability ARc.1319delTp.Leu440ArgfsTer19<100% 41/154 NM_014844​.5
NP_055659​.2
Zlotogora et al [2018], Neuser et al [2021]
THG1L Spinocerebellar ataxia type 28 (OMIM 618800)ARc.164T>Cp.Val55Ala~100% 31/110 to 1/130 NM_017872​.5
NP_060342​.2
Zlotogora et al [2018]
TKT Short stature, developmental delay, & congenital heart defects (OMIM 606781)ARc.769_770insCTACCTCCTTATCTTp.Trp257delinsSerThrSerLeuSerSerGly~100% 31/169 to 1/625 NM_001135055​.3
NP_001128527​.1
TMEM216 Joubert syndrome ARc.218G>Tp.Arg73Leu~100% 31/92 to 1/143 NM_001173990​.3
NP_001167461​.1
Edvardson et al [2010], Valente et al [2010], Zlotogora et al [2018]
TSPEAR Ectodermal dysplasia (OMIM 618180)ARc.1915G>Ap.Asp639Asn98%1/93 NM_144991​.3
NP_659428​.2
Zlotogora et al [2018]
VPS11 Hypomyelination & developmental delay (OMIM 616683)ARc. 2536T>Gp.Cys846Gly~100% 31/159 to 1/204 NM_021729​.6
NP_068375​.3

Included if ≤3 pathogenic variants account for ≥50% of variants identified in a specific ethnic group

AD = autosomal dominant; AR = autosomal recessive; MOI = mode of inheritance; NA = not applicable

1.

This percentage does not account for the possibility of rare de novo pathogenic variants occurring in this population.

2.
3.

To date, additional pathogenic variants in this gene have not been reported in individuals of Ashkenazi Jewish descent.

4.

At least one additional variant reported in this population in ≥1 family

5.

Does not conform to standard HGVS nomenclature

6.

RTEL1 variant c.3791G>A affects transcript variant rtel1at, an isoform of RTEL1.

Revision History

  • 20 October 2022 (sw) Revision: edited based on information in Zlotogora et al [2018]
  • 13 December 2018 (sw) Initial posting

References

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