Entity Name Entity type Gene Symbol Sources(; separated) Level4 Level3 Level2 Model_Of_Inheritance Phenotypes Omim Orphanet HPO Publications Description Flagged GEL_Status UserRatings_Green_amber_red version ready Mode of pathogenicity EnsemblId(GRch37) EnsemblId(GRch38) HGNC Position Chromosome Position GRCh37 Start Position GRCh37 End Position GRCh38 Start Position GRCh38 End STR Repeated Sequence STR Normal Repeats STR Pathogenic Repeats Region Haploinsufficiency Score Region Triplosensitivity Score Region Required Overlap Percentage Region Variant Type Region Verbose Name ALK gene ALK Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Spastic-dystonic diplegia 32989326 False 2 0;100;0 8.46 False ENSG00000171094 ENSG00000171094 HGNC:427 AMPD2 gene AMPD2 Expert list;Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal ?Spastic paraplegia 63, 615686, AR;Pontocerebellar hypoplasia, type 9, 615809, AR Novarino et al. (2014);24482476;27159321 False 2 33;67;0 8.46 False ENSG00000116337 ENSG00000116337 HGNC:469 ATAD3A gene ATAD3A Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Harel-Yoon syndrome, OMIM:617183;Spastic paraplegia 28158749;27640307;33845882;34387651 False 2 50;0;50 8.46 False ENSG00000197785 ENSG00000197785 HGNC:25567 BHLHE22 gene BHLHE22 Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Neurodevelopmental disorder, MONDO:0700092 39502664 False 2 100;0;0 8.46 False ENSG00000180828 ENSG00000180828 HGNC:11963 BLOC1S1 gene BLOC1S1 Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal severe intellectual disability;severe global developmental delay;epilepsy 33875846 False 2 100;0;0 8.46 False ENSG00000135441 ENSG00000135441 HGNC:4200 BORCS5 gene BORCS5 Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal arthrogryposis multiplex congenita, MONDO:0015168;neurodevelopmental disorder, MONDO:0700092 27435318;40385417;40621786 False 2 100;0;0 8.46 False ENSG00000165714 ENSG00000165714 HGNC:17950 CCDC82 gene CCDC82 Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal neurodevelopmental disorder, MONDO:0700092;hereditary spastic paraplegia, MONDO:0019064 35118659;35373332 False 2 0;100;0 8.46 False ENSG00000149231 ENSG00000149231 HGNC:26282 CHP1 gene CHP1 Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic ataxia 9, autosomal recessive, OMIM:618438 23904602;29379881;32787936 False 2 0;100;0 8.46 False ENSG00000187446 ENSG00000187446 HGNC:17433 DSTYK gene DSTYK Expert Review Amber;London North GLH;NHS GMS;Other;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology BOTH monoallelic and biallelic, autosomal or pseudoautosomal Spastic paraplegia 23, 270750;ongenital anomalies of kidney and urinary tract 1, 610805, AD;Spastic paraplegia 23, 270750, AR 28157540 False 2 33;67;0 8.46 False ENSG00000133059 ENSG00000133059 HGNC:29043 EXOSC3 gene EXOSC3 Expert list;Expert Review Amber Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Complicated hereditary spastic paraplegia 25149867;23975261 False 2 0;100;0 8.46 False ENSG00000107371 ENSG00000107371 HGNC:17944 FBXO31 gene FBXO31 Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted neurodevelopmental disorder, MONDO:0700092;Spasticity, HP:0001257;?Intellectual developmental disorder, autosomal recessive 45, OMIM:615979 24623383;32989326;33675180;35019165;41640354;41640354 False 2 100;0;0 8.46 False ENSG00000103264 ENSG00000103264 HGNC:16510 GAD1 gene GAD1 Expert Review Amber;NHS GMS;Radboud University Medical Center, Nijmegen;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Cerebralpalsy, spasticquadriplegic, 1, 603513 False 2 0;100;0 8.46 False ENSG00000128683 ENSG00000128683 HGNC:4092 GJC2 gene GJC2 Expert list;Expert Review Amber;London North GLH;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal ?Spastic paraplegia 44, autosomal recessive , OMIM:613206;Leukodystrophy, hypomyelinating, 2, OMIM:608804 19056803;22833003;31431325;37915394 False 2 25;50;25 8.46 False ENSG00000198835 ENSG00000198835 HGNC:17494 IBA57 gene IBA57 Expert Review Amber;Literature;London North GLH;NHS GMS;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal ?Spastic paraplegia 74, autosomal recessive, OMIM:616451 30258207;25609768 False 2 50;50;0 8.46 False ENSG00000181873 ENSG00000181873 HGNC:27302 LSM7 gene LSM7 Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Leukodystrophy, MONDO:0019046 35047835;39420558 False 2 0;0;100 8.46 False ENSG00000130332 ENSG00000130332 HGNC:20470 LYST gene LYST Expert Review Amber;Literature;London North GLH;NHS GMS;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal spastic paraplegia;Chediak-Higashi syndrome, 214500 24521565;26307451;25519961;25519960 False 2 33;67;0 8.46 False ENSG00000143669 ENSG00000143669 HGNC:1968 MARS2 gene MARS2 Expert Review Amber;London North GLH;NHS GMS;Radboud University Medical Center, Nijmegen;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic ataxia 3, autosomal recessive, 611390 22448145 False 2 67;33;0 8.46 False ENSG00000247626 ENSG00000247626 HGNC:25133 MTPAP gene MTPAP Expert Review Amber;London North GLH;NHS GMS;Radboud University Medical Center, Nijmegen;UKGTN;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Ataxia, spastic, 4;Spastic ataxia 4, autosomal recessive;?Spastic ataxia 4, autosomal recessive, 613672 20970105;27391121 False 2 33;67;0 8.46 False ENSG00000107951 ENSG00000107951 HGNC:25532 NRCAM gene NRCAM Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder with neuromuscular and skeletal abnormalities, OMIM:619833 35108495 False 2 100;0;0 8.46 False ENSG00000091129 ENSG00000091129 HGNC:7994 PI4KA gene PI4KA Expert Review Amber Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531 25855803;34415322;34415310 False 2 33;67;0 8.46 False ENSG00000241973 ENSG00000241973 HGNC:8983 POLR3K gene POLR3K Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Leukodystrophy, hypomyelinating, 21, OMIM:619310 30584594;33659930 False 2 0;100;0 8.46 False ENSG00000161980 ENSG00000161980 HGNC:14121 PTPN1 gene PTPN1 Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Encephalopathy, HP:0001298;dystonia, early-onset, and/or spastic paraplegia, MONDO:0859215 10066179;39986310 False 2 100;0;0 8.46 False ENSG00000196396 ENSG00000196396 HGNC:9642 RHOB gene RHOB Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Cerebral palsy 32989326 False 2 0;100;0 8.46 False Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments ENSG00000143878 ENSG00000143878 HGNC:668 RPS6KC1 gene RPS6KC1 Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal neurodevelopmental disorder, MONDO:0700092 41130203 False 2 100;0;0 8.46 False ENSG00000136643 ENSG00000136643 HGNC:10439 SARS2 gene SARS2 Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Hyperuricemia, pulmonary hypertension, renal failure, and alkalosis 613845;Progressive Spastic Paresis 21255763;24034276;27279129 False 2 0;100;0 8.46 False ENSG00000104835 ENSG00000104835 HGNC:17697 SLC25A46 gene SLC25A46 Expert Review Amber;Literature;London North GLH;NHS GMS;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Neuropathy, hereditary motor and sensory, type VIB, 616505 28369803;26168012 False 2 0;33;67 8.46 False ENSG00000164209 ENSG00000164209 HGNC:25198 TBCB gene TBCB Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder, MONDO:0700092 40856104 False 2 0;100;0 8.46 False ENSG00000105254 ENSG00000105254 HGNC:1989 TYW1 gene TYW1 Expert Review Amber;Literature Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal cerebral palsy, MONDO:0006497 34077496 False 2 0;100;0 8.46 False ENSG00000198874 ENSG00000198874 HGNC:25598 VAMP1 gene VAMP1 Expert Review Amber;London North GLH;NHS GMS;Radboud University Medical Center, Nijmegen;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Spastic ataxia 1, autosomal dominant, 108600 22958904;27957547 False 2 33;67;0 8.46 False ENSG00000139190 ENSG00000139190 HGNC:12642 VPS37A gene VPS37A Expert list;Expert Review Amber;London North GLH;NHS GMS;Radboud University Medical Center, Nijmegen;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 53, 614898, AR Zivony-Elboum et al. (2012);22717650 False 2 33;33;33 8.46 False ENSG00000155975 ENSG00000155975 HGNC:24928 WDR48 gene WDR48 Expert list;Expert Review Amber;NHS GMS;Yorkshire and North East GLH Childhood onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal spastic paraplegia Novarino et al. (2014);24482476 False 2 0;100;0 8.46 False ENSG00000114742 ENSG00000114742 HGNC:30914 ATXN1_CAG str ATXN1 NHS GMS;Expert Review Amber;Expert list Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Spinocerebellar ataxia 1, OMIM:164400 False 2 0;100;0 8.46 False ENSG00000124788 ENSG00000124788 HGNC:10548 6 16327867 16327953 16327636 16327722 CAG 36 45 ATXN2_CAG str ATXN2 NHS GMS;Expert Review Amber;Expert list Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Spinocerebellar ataxia 2, OMIM:183090;{Amyotrophic lateral sclerosis, susceptibility to, 13}, OMIM:183090 False 2 0;100;0 8.46 False ENSG00000204842 ENSG00000204842 HGNC:10555 12 112036755 112036823 111598951 111599019 CAG 32 35 ATXN3_CAG str ATXN3 NHS GMS;Expert Review Amber;Expert list Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Machado-Joseph disease, OMIM:109150 False 2 0;100;0 8.46 False ENSG00000066427 ENSG00000066427 HGNC:7106 14 92537355 92537396 92071011 92071052 CAG 45 60 ATXN7_CAG str ATXN7 NHS GMS;Expert Review Amber;Expert list Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Spinocerebellar ataxia 7, OMIM:164500 False 2 0;100;0 8.46 False ENSG00000163635 ENSG00000163635 HGNC:10560 3 63898362 63898391 63912686 63912715 CAG 28 37 CACNA1A_CAG str CACNA1A NHS GMS;Expert Review Amber;Expert list Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Spinocerebellar ataxia 6, OMIM:183086 9311738;18285829;19817876;16595610;8988170 False 2 0;100;0 8.46 False ENSG00000141837 ENSG00000141837 HGNC:1388 19 13318673 13318711 13207859 13207897 CAG 19 20 PPP2R2B_CAG str PPP2R2B NHS GMS;Expert Review Amber;Expert list Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Spinocerebellar ataxia 12, OMIM:604326 False 2 0;100;0 8.46 False ENSG00000156475 ENSG00000156475 HGNC:9305 5 146258292 146258321 146878729 146878758 CAG 33 43 TBP_CAG str TBP NHS GMS;Expert Review Amber;Expert list Childhood onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Spinocerebellar ataxia 17, OMIM:607136 False 2 100;0;0 8.46 False ENSG00000112592 ENSG00000112592 HGNC:11588 6 170870996 170871109 170561908 170562021 CAG 41 49