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 AFG3L2 gene AFG3L2 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic ataxia 5, autosomal recessive, OMIM:614487 False 2 25;50;25 6.9 False ENSG00000141385 ENSG00000141385 HGNC:315 AIMP1 gene AIMP1 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Leukodystrophy, hypomyelinating, 3, OMIM:260600 21092922;30477741;30486714 False 2 25;50;25 6.9 False ENSG00000164022 ENSG00000164022 HGNC:10648 ALS2 gene ALS2 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Amyotrophic lateral sclerosis 2, juvenile, OMIM:205100;Primary lateral sclerosis, juvenile, OMIM:606353 12145748;15247254;27601211 False 2 25;50;25 6.9 False ENSG00000003393 ENSG00000003393 HGNC:443 AMPD2 gene AMPD2 Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal ?Spastic paraplegia 63, 615686, AR;Hereditary Spastic Paraplegia?;Pontocerebellar hypoplasia, type 9, 615809, AR;Pontocerebellar hypolplasia (biallelic) Novarino et al. (2014);24482476;27159321 False 2 25;50;25 6.9 False ENSG00000116337 ENSG00000116337 HGNC:469 AP4B1 gene AP4B1 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 47, autosomal recessive, OMIM:614066;Hereditary spastic paraplegia 47, MONDO:0013551 21620353;24700674 False 2 20;60;20 6.9 False ENSG00000134262 ENSG00000134262 HGNC:572 AP4E1 gene AP4E1 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 51, autosomal recessive, OMIM:613744;Hereditary spastic paraplegia 51, MONDO:0013401 20972249;21620353;21937992;32979048 False 2 20;60;20 6.9 False ENSG00000081014 ENSG00000081014 HGNC:573 AP4M1 gene AP4M1 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 50, autosomal recessive, 612936 19559397;24700674;29096665 False 2 20;60;20 6.9 False ENSG00000221838 ENSG00000221838 HGNC:574 AP4S1 gene AP4S1 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal developmental delay;seizures;Spastic paraplegia 52, autosomal recessive, 614067 21620353;27444738;25552650 False 2 20;60;20 6.9 False ENSG00000100478 ENSG00000100478 HGNC:575 ARG1 gene ARG1 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Progressive spastic tetraplegia;Argininaemia, 207800 2365823;1463019;23859858 False 2 25;50;25 6.9 False ENSG00000118520 ENSG00000118520 HGNC:663 ARL6IP1 gene ARL6IP1 Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 61, autosomal recessive, 615685 24482476;28471035 False 2 67;33;0 6.9 False ENSG00000170540 ENSG00000170540 HGNC:697 C12orf65 gene C12orf65 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 55, autosomal recessive, OMIM:615035 23188110;24080142;24198383;24284555;24424123;25995486;26380172 False 2 20;60;20 6.9 False ENSG00000130921 ENSG00000130921 HGNC:26784 CHP1 gene CHP1 Expert Review Amber;Literature Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic ataxia 9, autosomal recessive, OMIM:618438 23904602;29379881;32787936 False 2 0;100;0 6.9 False ENSG00000187446 ENSG00000187446 HGNC:17433 CYP2U1 gene CYP2U1 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 56, autosomal recessive OMIM:615030;hereditary spastic paraplegia 56 MONDO:0014015 23176821;24337409 False 2 20;60;20 6.9 False ENSG00000155016 ENSG00000155016 HGNC:20582 DSTYK gene DSTYK Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Spastic paraplegia 23, 270750, AR;Spastic paraplegia 23, 270750;Congenital anomalies of kidney and urinary tract 1, 610805, AD 28157540 False 2 25;75;0 6.9 False ENSG00000133059 ENSG00000133059 HGNC:29043 ENTPD1 gene ENTPD1 Expert Review Amber;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 64, autosomal recessive, OMIM:615683 24482476;29691679;30652007 False 2 25;50;25 6.9 False ENSG00000138185 ENSG00000138185 HGNC:3363 ERLIN1 gene ERLIN1 Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Hereditary spastic paraplegia;Spastic paraplegia 62, 615681 24482476 False 2 20;60;20 6.9 False ENSG00000107566 ENSG00000107566 HGNC:16947 FARS2 gene FARS2 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 77, autosomal recessive, 617046 False 2 25;50;25 6.9 False ENSG00000145982 ENSG00000145982 HGNC:21062 GAD1 gene GAD1 Expert Review Amber;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Cerebralpalsy, spasticquadriplegic,1, 603513 15571623, 28454995 False 2 0;100;0 6.9 False ENSG00000128683 ENSG00000128683 HGNC:4092 GJC2 gene GJC2 Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult 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 60;40;0 6.9 False ENSG00000198835 ENSG00000198835 HGNC:17494 HACE1 gene HACE1 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal seizure;Spastic paraplegia and psychomotor retardation with or without seizures, 616756;psychomotor retardation;Spastic paraplegia 26424145;26437029;29423242;31321300;33813722 False 2 25;50;25 6.9 False ENSG00000085382 ENSG00000085382 HGNC:21033 HSPD1 gene HSPD1 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Spastic paraplegia 13, autosomal dominant, OMIM:605280 10677329;11898127;17420924 False 2 0;100;0 6.9 False ENSG00000144381 ENSG00000144381 HGNC:5261 IBA57 gene IBA57 Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal ?Spastic paraplegia 74, autosomal recessive, OMIM:616451 30258207;25609768 False 2 25;50;25 6.9 False ENSG00000181873 ENSG00000181873 HGNC:27302 KDM5C gene KDM5C Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Intellectual developmental disorder, X-linked syndromic, Claes-Jensen type, OMIM:300534 10982473;15586325;18697827;19826449;26919706;32279304 False 2 33;50;17 6.9 False ENSG00000126012 ENSG00000126012 HGNC:11114 KIDINS220 gene KIDINS220 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Spastic paraplegia, intellectual disability, nystagmus, and obesity, OMIM:617296 27005418;29667355;31630374 False 2 25;50;25 6.9 False ENSG00000134313 ENSG00000134313 HGNC:29508 L1CAM gene L1CAM Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology X-LINKED: hemizygous mutation in males, biallelic mutations in females CRASH syndrome, OMIM:303350;MASA syndrome, OMIM:303350;Hydrocephalus due to aqueductal stenosis, OMIM:307000;Hydrocephalus with congential idiopathic intestinal pseudoobstruction, OMIM:307000;Hydrocephalus with Hirschsprung disease, OMIM:307000 7920659;7920660;7562969 False 2 25;50;25 6.9 False ENSG00000198910 ENSG00000198910 HGNC:6470 LYST gene LYST Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal spastic paraplegia;Chediak-Higashi syndrome, 214500;Spastic paraplegia 24521565;26307451;25519961;25519960 False 2 25;75;0 6.9 False ENSG00000143669 ENSG00000143669 HGNC:1968 MARS2 gene MARS2 Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic ataxia 3, autosomal recessive, 611390;Spastic ataxia 3, autosomal recessive Bayat (2012), 22448145 False 2 50;50;0 6.9 False ENSG00000247626 ENSG00000247626 HGNC:25133 MTPAP gene MTPAP Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Ataxia, spastic, 4;?Spastic ataxia 4, autosomal recessive, 613672;Spastic ataxia 4, autosomal recessive 20970105;27391121 False 2 25;75;0 6.9 False ENSG00000107951 ENSG00000107951 HGNC:25532 NKX6-2 gene NKX6-2 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy, 617560 28575651;15601927;29388673 False 2 25;50;25 6.9 False ENSG00000148826 ENSG00000148826 HGNC:19321 NT5C2 gene NT5C2 Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 45, autosomal recessive, 613162 19415352;24482476;28327087;28884889;29123918;32153630 False 2 40;40;20 6.9 False ENSG00000076685 ENSG00000076685 HGNC:8022 RAB3GAP2 gene RAB3GAP2 Expert Review Amber;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Martsolf syndrome 1, OMIM:212720;Warburg micro syndrome 2, OMIM:614225 24482476;32740904 False 2 25;25;50 6.9 False ENSG00000118873 ENSG00000118873 HGNC:17168 REEP2 gene REEP2 Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BOTH monoallelic and biallelic, autosomal or pseudoautosomal ?Spastic paraplegia 72, autosomal dominant, 615625;?Spastic paraplegia 72, autosomal dominant,615625;?Spastic paraplegia 72, autosomal recessive, 615625 24388663;24482476;28491902;33526816 False 2 40;40;20 6.9 False ENSG00000132563 ENSG00000132563 HGNC:17975 SERAC1 gene SERAC1 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome, OMIM:614739 29205472;22683713;16527507;28482397;28778788;27186703;27604308 False 2 25;50;25 6.9 False ENSG00000122335 ENSG00000122335 HGNC:21061 SLC16A2 gene SLC16A2 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology X-LINKED: hemizygous mutation in males, biallelic mutations in females Allan-Herndon-Dudley syndrome, OMIM:300523 14661163;19194886;20713192;22805248;23419639;24170966;25755011;25900139;28742507;31410843 False 2 25;50;25 6.9 False ENSG00000147100 ENSG00000147100 HGNC:10923 SLC1A4 gene SLC1A4 Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic tetraplegia, thin corpus callosum, and progressive microcephaly, OMIM:616657 29989513;27193218;26138499;26041762;25930971 False 2 25;50;25 6.9 False ENSG00000115902 ENSG00000115902 HGNC:10942 SPART gene SPART Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Troyer syndrome, OMIM:275900;Spastic paraplegia 20 12134148;18413476;20301556;20437587;27112432;28679690 False 2 25;50;25 6.9 False ENSG00000133104 ENSG00000133104 HGNC:18514 TECPR2 gene TECPR2 Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 49, autosomal recessive, 615031;Spastic paraplegia 49, autosomal recessive,615031, AR 23176824;26542466 False 2 25;75;0 6.9 False ENSG00000196663 ENSG00000196663 HGNC:19957 TFG gene TFG Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 57, autosomal recessive, OMIM:615658 23479643;27492651;27601211;28124177;29971521;30467354;33767317 False 2 60;20;20 6.9 False ENSG00000114354 ENSG00000114354 HGNC:11758 TRMT5 gene TRMT5 Expert Review Amber;Literature Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Peripheral neuropathy with variable spasticity, exercise intolerance, and developmental delay, OMIM:616539 26189817;29021354 False 2 0;100;0 6.9 False ENSG00000126814 ENSG00000126814 HGNC:23141 VAMP1 gene VAMP1 Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Spastic ataxia 1, autosomal dominant, 108600 22958904;27957547 False 2 25;50;25 6.9 False ENSG00000139190 ENSG00000139190 HGNC:12642 VPS37A gene VPS37A Expert Review Amber;London North GLH;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia 53, autosomal recessive;Spastic paraplegia 53, autosomal recessive, 614898, AR Zivony-Elboum et al. (2012);22717650 False 2 25;25;50 6.9 False ENSG00000155975 ENSG00000155975 HGNC:24928 WDR45B gene WDR45B Expert Review Amber;London North GLH;NHS GMS;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Neurodevelopmental disorder with spastic quadriplegia and brain abnormalities with or without seizures, OMIM:617977 21937992;28503735 False 2 25;50;25 6.9 False ENSG00000141580 ENSG00000141580 HGNC:25072 WDR48 gene WDR48 Expert Review Amber;NHS GMS;South West GLH;Yorkshire and North East GLH Adult onset hereditary spastic paraplegia Neurology BIALLELIC, autosomal or pseudoautosomal Spastic paraplegia Novarino et al. (2014);24482476;24482476 False 2 0;100;0 6.9 False ENSG00000114742 ENSG00000114742 HGNC:30914