SPG7 (Q9UQ90) variants and mutations
SPG7 (also known as Q9UQ90) is a human protein-coding gene encoding a mitochondrial inner membrane m-AAA protease component paraplegin protein. It participates in mitochondrial inner-membrane protein quality control and respiratory homeostasis as part of the m-AAA protease machinery. Biallelic pathogenic variants cause SPG7-related disease, commonly presenting with spastic ataxia, optic neuropathy, or progressive gait impairment. This analysis covers 1,377 SPG7 variants and mutations. Of these, 88% have computational variant effect predictions. Disease context includes Autosomal recessive spastic paraplegia type 7, hereditary spastic paraplegia 7, and hereditary spastic paraplegia. Example SPG7 variants include M1I, M1K, and M1R.
Variant analysis overview
- Gene: SPG7
- Protein: Q9UQ90
- UniProt accession: Q9UQ90
- Organism: Homo sapiens
- Variants analyzed: 1377
- Variant scope: all variants
- Completed: 2026-08-22
Variant and mutation evidence
- Variant composition: 1,146 unspecified-consequence records; 148 missense variants; 56 synonymous variants; 15 frameshift variants; 2 in-frame insertions; 4 in-frame deletions; 5 stop-gained variants; 1 splice-region variants; 2 substitution
- Prediction scores: 1,212 variants have prediction scores (88% of the analyzed set).
Clinical, disease, and population context
- Disease context: 25 disease associations are represented. Top associations: Autosomal recessive spastic paraplegia type 7, hereditary spastic paraplegia 7, hereditary spastic paraplegia, hereditary disease, Spastic paraplegia, mitochondrial disease, spastic ataxia, hereditary ataxia, Retinal dystrophy, Gait ataxia, Spastic paraparesis, Dysarthria.
Protein structure and variant hotspots
- Protein features: 2 transmembrane segments; 10 binding sites; 1 post-translational modification sites.
- Structural context: 46 variants have structural context.
Data sources
Evidence in this analysis draws on EBI Proteins Variation, UniProt, gnomAD v4, EuropePMC, Interaction Network Analysis, Protein Data Bank, AlphaFold DB, gnomAD constraint, Open Targets, ClinGen, MaveDB, LitVar.
Notable SPG7 variants
Examples include M1I, M1K, M1R, M1V, A2D, A2T, A2V, A2S. Listed records include available protein-change notation, database identifiers, clinical classifications, computational predictions, population evidence, experimental measurements, and disease context.
- M1I (p.Met1Ile), rs2543660604, ClinVar RCV004585107, ClinVar RCV004818487, Likely pathogenic, not provided; Hereditary spastic paraplegia 7
- M1K (p.Met1Lys), rs1332265538, ClinGen CA397415810, ClinVar RCV001382565, MetaLR 0.90, MetaSVM 0.96, Pathogenic/Likely pathogenic, Hereditary spastic paraplegia 7
- M1R (p.Met1Arg), rs1332265538, ClinGen CA397415808, ClinVar RCV003388959, MetaLR 0.90, MetaSVM 0.96, Pathogenic, Hereditary spastic paraplegia 7
- M1V (p.Met1Val), rs794726906, ClinGen CA274907, ClinVar RCV000173302, ClinVar RCV001852108, MetaLR 0.88, MetaSVM 0.86, Pathogenic/Likely pathogenic, SPG7-related disorder; not provided; Hereditary spastic paraplegia 7
- A2D (p.Ala2Asp), TOPMed rs973170664, gnomAD rs973170664, CADD 23.50, PolyPhen-2 0.80
- A2T (p.Ala2Thr), rs535030441, ClinGen CA321845, ClinVar RCV000817246, ClinVar RCV001722098, CADD 23.00, PolyPhen-2 0.35, Conflicting interpretations, Inborn genetic diseases; not specified; not provided
- A2V (p.Ala2Val), TOPMed rs973170664, gnomAD rs973170664, CADD 17.30, PolyPhen-2 0.01, Uncertain significance, Hereditary spastic paraplegia 7; Inborn genetic diseases
- A2S (p.Ala2Ser), gnomAD 16-89508421-G-T, CADD 22.80, PolyPhen-2 0.43
- A2A (p.Ala2Ala), rs1339691699, gnomAD 16-89508423-C-T, CADD 8.21
- V3A (p.Val3Ala), TOPMed rs2057958133, CADD 7.70, PolyPhen-2 0.00
- p.Val3dup, gnomAD 16-89508423-C-CGT, CADD 17.50
- V3L (p.Val3Leu), gnomAD 16-89508424-G-C, CADD 20.00, PolyPhen-2 0.00
- V3M (p.Val3Met), gnomAD 16-89508424-G-A, CADD 22.80, PolyPhen-2 0.02
- V3E (p.Val3Glu), gnomAD 16-89508425-T-A, CADD 17.80, PolyPhen-2 0.00
- V3V (p.Val3Val), rs553241838, gnomAD 16-89508426-G-T, CADD 0.30
- L4P (p.Leu4Pro), rs2057958357, ClinGen CA397415827, ClinVar RCV003617759, ClinVar RCV005281458, CADD 10.70, PolyPhen-2 0.00, Uncertain significance, Hereditary spastic paraplegia 7; Inborn genetic diseases
- L4R (p.Leu4Arg), TOPMed rs2057958357, gnomAD rs2057958357, CADD 10.40, PolyPhen-2 0.04, Uncertain significance
- L4V (p.Leu4Val), TOPMed rs2057958304, CADD 0.16, PolyPhen-2 0.00
- L4A (p.Leu4Ala), gnomAD 16-89508425-TGC-T, CADD 13.40
- L4M (p.Leu4Met), gnomAD 16-89508427-C-A, CADD 2.73, PolyPhen-2 0.00
- L4L (p.Leu4Leu), rs2057958304, gnomAD 16-89508427-C-T, CADD 2.93
- L4Q (p.Leu4Gln), gnomAD 16-89508428-T-A, CADD 10.20, PolyPhen-2 0.04
- L5P (p.Leu5Pro), gnomAD rs1488107055, CADD 19.60, PolyPhen-2 0.14
- L5C (p.Leu5Cys), gnomAD 16-89508428-TG-T, CADD 17.80
- L5M (p.Leu5Met), gnomAD 16-89508430-C-A, CADD 1.78, PolyPhen-2 0.14
- L5V (p.Leu5Val), gnomAD 16-89508430-C-G, CADD 6.24, PolyPhen-2 0.01
- L5L (p.Leu5Leu), rs952946941, gnomAD 16-89508430-C-T, CADD 1.88
- L5R (p.Leu5Arg), gnomAD 16-89508431-T-G, CADD 18.90, PolyPhen-2 0.04
- L6Q (p.Leu6Gln), gnomAD rs1352999079, CADD 22.90, Uncertain significance, Inborn genetic diseases
- L6L (p.Leu6Leu), rs1269380835, gnomAD 16-89508433-C-T, CADD 7.94
- L6V (p.Leu6Val), gnomAD 16-89508433-C-G, CADD 14.30, PolyPhen-2 0.09
- L6P (p.Leu6Pro), gnomAD 16-89508434-T-C, CADD 22.80, PolyPhen-2 0.00
- L7M (p.Leu7Met), rs1188029212, ClinGen CA397415840, ClinVar RCV001090548, TOPMed rs1188029212, CADD 17.00, PolyPhen-2 0.54, Uncertain significance, not provided
- L7P (p.Leu7Pro), TOPMed rs984633036, gnomAD rs984633036, CADD 22.90, PolyPhen-2 0.45
- L7V (p.Leu7Val), TOPMed rs1188029212, gnomAD rs1188029212, CADD 6.43, PolyPhen-2 0.01, Likely benign
- L7L (p.Leu7Leu), rs1188029212, gnomAD 16-89508436-C-T, CADD 4.98
- L8F (p.Leu8Phe), cosmic curated COSV10958, ExAC rs773745485, TOPMed rs773745485, gnomAD rs773745485, CADD 11.50, PolyPhen-2 0.07
- L8V (p.Leu8Val), ExAC rs773745485, TOPMed rs773745485, gnomAD rs773745485, CADD 9.39, PolyPhen-2 0.00
- p.Leu8dup, rs781285980, gnomAD 16-89508424-G-GTG, CADD 17.50
- L8del (p.Leu8del), rs781285980, gnomAD 16-89508424-GTGC-, CADD 12.50
- L8I (p.Leu8Ile), gnomAD 16-89508439-C-A, CADD 9.54, PolyPhen-2 0.01
- L8P (p.Leu8Pro), gnomAD 16-89508440-T-C, CADD 16.60, PolyPhen-2 0.00
- L8L (p.Leu8Leu), gnomAD 16-89508441-C-A, CADD 2.51
- R9C (p.Arg9Cys), rs1368314619, ClinGen CA397415849, ClinVar RCV001069528, ClinVar RCV002511031, CADD 22.60, PolyPhen-2 0.35, Uncertain significance, Inborn genetic diseases; Hereditary spastic paraplegia 7; not provided
- R9H (p.Arg9His), ExAC rs763469858, gnomAD rs763469858, CADD 20.20, PolyPhen-2 0.00
- R9P (p.Arg9Pro), ExAC rs763469858, gnomAD rs763469858, CADD 21.60, PolyPhen-2 0.32
- R9G (p.Arg9Gly), rs1186328599, gnomAD 16-89507706-GC-G, CADD 6.78
- R9W (p.Arg9Trp), gnomAD 16-89507708-C-T, CADD 7.17
- R9R (p.Arg9Arg), rs1235386861, gnomAD 16-89507708-C-A, CADD 6.56
- R9Q (p.Arg9Gln), rs1473634224, gnomAD 16-89507709-G-A, CADD 9.77
- R9K (p.Arg9Lys), rs1567889740, gnomAD 16-89507715-G-A, CADD 3.74
- R9S (p.Arg9Ser), gnomAD 16-89508442-C-A, CADD 20.00, PolyPhen-2 0.07
- R9L (p.Arg9Leu), gnomAD 16-89508443-G-T, CADD 16.50, PolyPhen-2 0.00
- A10G (p.Ala10Gly), TOPMed rs1392123787, gnomAD rs1392123787
- A10P (p.Ala10Pro), 1000Genomes rs577872969, TOPMed rs577872969, gnomAD rs577872969, CADD 3.91, PolyPhen-2 0.07, Uncertain significance, Hereditary spastic paraplegia 7; not provided
- A10S (p.Ala10Ser), rs577872969, ClinGen CA397415853, ClinVar RCV001972989, 1000Genomes rs577872969, CADD 0.43, PolyPhen-2 0.00, Uncertain significance, Hereditary spastic paraplegia 7
- A10T (p.Ala10Thr), rs577872969, ClinGen CA286519175, ClinVar RCV002781259, 1000Genomes rs577872969, CADD 0.76, PolyPhen-2 0.00, Uncertain significance, Hereditary spastic paraplegia 7
- A10V (p.Ala10Val), TOPMed rs1392123787, gnomAD rs1392123787, CADD 1.75, PolyPhen-2 0.00
- A10A (p.Ala10Ala), rs763741926, gnomAD 16-89507734-C-T, CADD 7.59
- A10D (p.Ala10Asp), gnomAD 16-89508446-C-A, CADD 5.51, PolyPhen-2 0.02
- L11F (p.Leu11Phe), TOPMed rs1206986382, gnomAD rs1206986382, CADD 17.10, PolyPhen-2 0.11
- L11P (p.Leu11Pro), rs943187212, ClinGen CA397415860, ClinVar RCV001059473, TOPMed rs943187212, CADD 21.40, PolyPhen-2 0.00, Uncertain significance, Hereditary spastic paraplegia 7
- L11R (p.Leu11Arg), TOPMed rs943187212, gnomAD rs943187212, CADD 20.70, PolyPhen-2 0.00, Uncertain significance
- L11V (p.Leu11Val), TOPMed rs1206986382, gnomAD rs1206986382, CADD 11.20, PolyPhen-2 0.00
- L11I (p.Leu11Ile), gnomAD 16-89508448-C-A, CADD 16.00, PolyPhen-2 0.01
- L11L (p.Leu11Leu), gnomAD 16-89508450-C-A, CADD 1.25
- R12C (p.Arg12Cys), TOPMed rs1038946809, gnomAD rs1038946809, CADD 21.90, PolyPhen-2 0.00
- R12H (p.Arg12His), TOPMed rs2057959338, CADD 18.10, PolyPhen-2 0.00
- R12S (p.Arg12Ser), gnomAD 16-89508451-C-A, CADD 19.10, PolyPhen-2 0.03
- R12G (p.Arg12Gly), gnomAD 16-89508451-C-G, CADD 19.60, PolyPhen-2 0.04
- R12L (p.Arg12Leu), gnomAD 16-89508452-G-T, CADD 14.50, PolyPhen-2 0.02
- R12R (p.Arg12Arg), rs1230229317, gnomAD 16-89508453-C-T, CADD 3.30
- R13G (p.Arg13Gly), rs923197967, ClinGen CA286519194, ClinVar RCV002139937, ClinVar RCV005742417, CADD 21.50, PolyPhen-2 0.02, Conflicting interpretations, Hereditary spastic paraplegia 7; Inborn genetic diseases
- R13W (p.Arg13Trp), TOPMed rs923197967, gnomAD rs923197967, CADD 22.70, PolyPhen-2 0.18, Uncertain significance, not provided; Hereditary spastic paraplegia 7
- R13R (p.Arg13Arg), gnomAD 16-89507726-C-A, CADD 1.24
- R13P (p.Arg13Pro), rs539971364, gnomAD 16-89507727-G-C, CADD 1.61
- R13L (p.Arg13Leu), gnomAD 16-89508455-G-T, CADD 2.75, PolyPhen-2 0.00
- R13Q (p.Arg13Gln), gnomAD 16-89508455-G-A, CADD 0.03, PolyPhen-2 0.00
- G14D (p.Gly14Asp), TOPMed rs1267090698, gnomAD rs1267090698, CADD 9.53, PolyPhen-2 0.05
- G14R (p.Gly14Arg), TOPMed rs1242380690, gnomAD rs1242380690, CADD 7.76, PolyPhen-2 0.00, Uncertain significance
- G14S (p.Gly14Ser), rs1242380690, ClinGen CA397415871, ClinVar RCV001201656, TOPMed rs1242380690, CADD 7.59, Uncertain significance, Hereditary spastic paraplegia 7
- G14C (p.Gly14Cys), gnomAD 16-89507693-G-T, CADD 9.40
- G14G (p.Gly14Gly), rs2057937523, gnomAD 16-89507695-C-G, CADD 9.20
- G14V (p.Gly14Val), rs767015197, gnomAD 16-89507712-G-T, CADD 4.53
- P15A (p.Pro15Ala), TOPMed rs757046310, gnomAD rs757046310, CADD 14.90, PolyPhen-2 0.00, Uncertain significance
- P15S (p.Pro15Ser), rs757046310, ClinGen CA286519206, ClinVar RCV003884323, TOPMed rs757046310, CADD 16.10, PolyPhen-2 0.01, Uncertain significance, not provided
- P15T (p.Pro15Thr), gnomAD 16-89508460-C-A, CADD 11.60, PolyPhen-2 0.02
- P15Q (p.Pro15Gln), gnomAD 16-89508461-C-A, CADD 9.15, PolyPhen-2 0.00
- P15P (p.Pro15Pro), gnomAD 16-89508462-A-G, CADD 3.46
- G16S (p.Gly16Ser), ExAC rs766810299, gnomAD rs766810299, CADD 14.30, PolyPhen-2 0.01
- G16R (p.Gly16Arg), gnomAD 16-89508463-G-C, CADD 14.70, PolyPhen-2 0.04
- G16C (p.Gly16Cys), gnomAD 16-89508463-G-T, CADD 16.00, PolyPhen-2 0.17
- G16V (p.Gly16Val), gnomAD 16-89508464-G-T, CADD 17.20, PolyPhen-2 0.02
- G16D (p.Gly16Asp), gnomAD 16-89508464-G-A, CADD 13.90, PolyPhen-2 0.00
- G16G (p.Gly16Gly), gnomAD 16-89508465-C-A, CADD 1.31
- P17L (p.Pro17Leu), rs956304326, ClinGen CA286519225, ClinVar RCV002595782, TOPMed rs956304326, CADD 4.03, PolyPhen-2 0.00, Uncertain significance, Hereditary spastic paraplegia 7
- P17Q (p.Pro17Gln), rs956304326, ClinGen CA397415889, ClinVar RCV001356438, TOPMed rs956304326, CADD 8.02, PolyPhen-2 0.07, Uncertain significance, not provided
- P17R (p.Pro17Arg), rs956304326, ClinGen CA397415890, ClinVar RCV001848241, ClinVar RCV001885411, CADD 7.55, PolyPhen-2 0.05, Uncertain significance, Hereditary spastic paraplegia 7; not provided; Hereditary spastic paraplegia
- P17S (p.Pro17Ser), TOPMed rs1031899714, gnomAD rs1031899714, CADD 0.74, PolyPhen-2 0.00
- P17T (p.Pro17Thr), gnomAD 16-89508466-C-A, CADD 0.70, PolyPhen-2 0.00
- P17P (p.Pro17Pro), gnomAD 16-89508468-G-C, CADD 1.93
- G18S (p.Gly18Ser), rs2057959836, ClinGen CA397415891, ClinVar RCV003618116, Ensembl rs2057959836, AlphaMissense 0.17, MetaLR 0.46, Uncertain significance, Hereditary spastic paraplegia 7
- G18V (p.Gly18Val), rs1371729405, ClinGen CA397415896, ClinVar RCV000517403, TOPMed rs1371729405, CADD 18.70, PolyPhen-2 0.06, Uncertain significance, not specified
- p.Gly18 Pro27del, gnomAD 16-89508454-CGGGG, CADD 13.70
- G18C (p.Gly18Cys), gnomAD 16-89508469-G-T, CADD 19.50, PolyPhen-2 0.32
- G18D (p.Gly18Asp), gnomAD 16-89508470-G-A, CADD 18.90, PolyPhen-2 0.00
- G18G (p.Gly18Gly), gnomAD 16-89508471-T-C, CADD 6.18
- P19R (p.Pro19Arg), Ensembl rs2152392865, CADD 6.42, PolyPhen-2 0.02
- P19S (p.Pro19Ser), gnomAD rs1466413332, CADD 7.43, PolyPhen-2 0.00
- P19G (p.Pro19Gly), rs2057959670, gnomAD 16-89508459-TCCAG, CADD 24.60
- p.Pro19 Pro37del, gnomAD 16-89508471-TCCTC, CADD 15.80
- P19T (p.Pro19Thr), gnomAD 16-89508472-C-A, CADD 9.35, PolyPhen-2 0.00
- P19H (p.Pro19His), gnomAD 16-89508473-C-A, CADD 8.56, PolyPhen-2 0.12
- P19P (p.Pro19Pro), rs1555608404, gnomAD 16-89508474-T-C, CADD 6.36
- R20W (p.Arg20Trp), rs863224222, ClinGen CA321596, ClinVar RCV000197155, Ensembl rs863224222, CADD 13.40, PolyPhen-2 0.00, Uncertain significance, not provided
- p.Arg20 Pro31del, gnomAD 16-89508469-GGTCC, CADD 16.10
- R20Q (p.Arg20Gln), gnomAD 16-89508476-G-A, CADD 9.34, PolyPhen-2 0.01
- R20L (p.Arg20Leu), gnomAD 16-89508476-G-T, CADD 8.99, PolyPhen-2 0.00
- R20R (p.Arg20Arg), rs1187276565, gnomAD 16-89508477-G-A, CADD 7.76
- P21L (p.Pro21Leu), gnomAD rs1255749117, CADD 13.80, PolyPhen-2 0.00
- P21R (p.Pro21Arg), gnomAD rs1255749117
- P21T (p.Pro21Thr), gnomAD 16-89508478-C-A, CADD 4.68, PolyPhen-2 0.00
- P21S (p.Pro21Ser), gnomAD 16-89508478-C-T, CADD 5.88, PolyPhen-2 0.00
- P21Q (p.Pro21Gln), gnomAD 16-89508479-C-A, CADD 11.20, PolyPhen-2 0.01
- P21P (p.Pro21Pro), rs932959782, gnomAD 16-89508480-G-A, CADD 6.27
- L22P (p.Leu22Pro), gnomAD 16-89508482-T-C, CADD 20.60, PolyPhen-2 0.01
- L22L (p.Leu22Leu), rs1167383291, gnomAD 16-89508483-G-C, CADD 2.33
- W23* (p.Trp23Ter), rs1457238867, ClinGen CA397415924, ClinVar RCV003391406, ClinVar RCV003482463, CADD 37.00, Likely pathogenic
- W23C (p.Trp23Cys), gnomAD rs1457238867, CADD 23.40, PolyPhen-2 0.24, Likely pathogenic
- W23G (p.Trp23Gly), TOPMed rs1419170613, gnomAD rs1419170613, CADD 19.10, PolyPhen-2 0.02
- W23R (p.Trp23Arg), TOPMed rs1419170613, gnomAD rs1419170613, CADD 13.40, PolyPhen-2 0.00
- W23L (p.Trp23Leu), gnomAD 16-89508485-G-T, CADD 21.50, PolyPhen-2 0.01
- G24A (p.Gly24Ala), ExAC rs774999325, TOPMed rs774999325, gnomAD rs774999325, CADD 17.20, PolyPhen-2 0.00
- G24V (p.Gly24Val), ExAC rs774999325, TOPMed rs774999325, gnomAD rs774999325, CADD 21.80, PolyPhen-2 0.03
- G24S (p.Gly24Ser), gnomAD 16-89508487-G-A, CADD 16.00, PolyPhen-2 0.00
- G24C (p.Gly24Cys), gnomAD 16-89508487-G-T, CADD 20.70, PolyPhen-2 0.00
- G24D (p.Gly24Asp), gnomAD 16-89508488-G-A, CADD 21.90, PolyPhen-2 0.04
- G24G (p.Gly24Gly), gnomAD 16-89508489-C-G, CADD 10.10
- P25A (p.Pro25Ala), TOPMed rs1379498694, gnomAD rs1379498694, CADD 0.73, PolyPhen-2 0.00
- P25Q (p.Pro25Gln), gnomAD 16-89508488-GC-G, CADD 23.20
- P25T (p.Pro25Thr), gnomAD 16-89508490-C-A, CADD 3.05, PolyPhen-2 0.01
- P25S (p.Pro25Ser), gnomAD 16-89508490-C-T, CADD 2.90, PolyPhen-2 0.00
- P25L (p.Pro25Leu), gnomAD 16-89508491-C-T, CADD 3.76, PolyPhen-2 0.00
- P25P (p.Pro25Pro), rs760168945, gnomAD 16-89508492-A-C, CADD 5.12
- G26C (p.Gly26Cys), rs763721899, ClinGen CA286519237, ClinVar RCV001233635, ClinVar RCV003482351, CADD 14.30, PolyPhen-2 0.00, Uncertain significance, Inborn genetic diseases; Hereditary spastic paraplegia 7; not provided
- G26R (p.Gly26Arg), 1000Genomes rs763721899, ExAC rs763721899, TOPMed rs763721899, gnomAD rs763721899, CADD 12.00, PolyPhen-2 0.00, Uncertain significance, Inborn genetic diseases
- G26S (p.Gly26Ser), gnomAD 16-89508493-G-A, CADD 11.10, PolyPhen-2 0.01
- G26V (p.Gly26Val), gnomAD 16-89508494-G-T, CADD 5.67, PolyPhen-2 0.00
- G26A (p.Gly26Ala), gnomAD 16-89508494-G-C, CADD 4.61, PolyPhen-2 0.00
- G26D (p.Gly26Asp), gnomAD 16-89508494-G-A, CADD 7.84, PolyPhen-2 0.00
- G26G (p.Gly26Gly), gnomAD 16-89508495-C-A, CADD 7.45
- P27Q (p.Pro27Gln), rs878854605, ClinGen CA397415945, ClinVar RCV002630892, AlphaMissense 0.07, MetaLR 0.53, Uncertain significance, Hereditary spastic paraplegia 7
- P27R (p.Pro27Arg), rs878854605, ClinGen CA10583433, ClinVar RCV000231137, ClinVar RCV003243025, AlphaMissense 0.07, MetaLR 0.53, Uncertain significance, Inborn genetic diseases; not provided; Hereditary spastic paraplegia 7
- P27S (p.Pro27Ser), Ensembl rs2057960481
- P27L (p.Pro27Leu), gnomAD 16-89508497-C-T, CADD 0.84, PolyPhen-2 0.00
- P27P (p.Pro27Pro), rs753537336, gnomAD 16-89508498-G-A, CADD 2.48
- A28P (p.Ala28Pro), ExAC rs757013711, gnomAD rs757013711, CADD 13.00, PolyPhen-2 0.02, Uncertain significance, not provided
- A28S (p.Ala28Ser), ExAC rs757013711, gnomAD rs757013711, CADD 2.95, PolyPhen-2 0.00
- A28T (p.Ala28Thr), rs757013711, ClinGen CA397415947, ClinVar RCV003317833, CADD 6.94, PolyPhen-2 0.00, Uncertain significance, not specified
- A28G (p.Ala28Gly), rs2057960339, gnomAD 16-89508489-CCCAG, CADD 23.60
- A28D (p.Ala28Asp), gnomAD 16-89508500-C-A, CADD 5.04, PolyPhen-2 0.01
- A28V (p.Ala28Val), gnomAD 16-89508500-C-T, CADD 6.12, PolyPhen-2 0.01
- A28A (p.Ala28Ala), gnomAD 16-89508501-C-G, CADD 8.71
- W29* (p.Trp29Ter), rs1597597437, ClinGen CA397415958, ClinVar RCV000850308, ClinVar RCV001391422, CADD 23.20, Pathogenic
- W29R (p.Trp29Arg), gnomAD 16-89508502-T-C, CADD 9.08, PolyPhen-2 0.00
- W29L (p.Trp29Leu), gnomAD 16-89508503-G-T, CADD 17.10, PolyPhen-2 0.01
- W29C (p.Trp29Cys), gnomAD 16-89508504-G-T, CADD 22.40, PolyPhen-2 0.17
- S30N (p.Ser30Asn), rs863224215, ClinGen CA323832, ClinVar RCV000389351, ClinVar RCV003417714, CADD 7.14, PolyPhen-2 0.00, Uncertain significance, SPG7-related disorder; Hereditary spastic paraplegia 7
- S30R (p.Ser30Arg), rs2543661779, ClinGen CA397415967, ClinVar RCV003618172, Uncertain significance, Hereditary spastic paraplegia 7
- S30L (p.Ser30Leu), rs373897303, gnomAD 16-89507697-C-T, CADD 3.02
- S30W (p.Ser30Trp), gnomAD 16-89507697-C-G, CADD 2.50
- S30S (p.Ser30Ser), rs1466810011, gnomAD 16-89507698-G-A, CADD 2.09
- S30I (p.Ser30Ile), rs914604016, gnomAD 16-89507703-G-T, CADD 5.08
- S30G (p.Ser30Gly), rs1430852191, gnomAD 16-89507729-A-G, CADD 2.74
- S30P (p.Ser30Pro), rs201673225, gnomAD 16-89507732-GC-G, CADD 3.56
- S30A (p.Ser30Ala), gnomAD 16-89507735-T-G, CADD 4.04
- S30F (p.Ser30Phe), rs1342505761, gnomAD 16-89507736-C-T, CADD 6.97
- S30C (p.Ser30Cys), rs1342505761, gnomAD 16-89507736-C-G, CADD 6.53
- S30K (p.Ser30Lys), gnomAD 16-89507740-G-GA, CADD 3.64
- P31S (p.Pro31Ser), gnomAD 16-89508508-C-T, CADD 10.30, PolyPhen-2 0.00
Public SPG7 analysis runs
- SPG7 analysis run — SPG7 (1,377 variants) — completed 2026-08-22