SPG11

SPG11 vesicle trafficking associated, spatacsin

Basic information

Region (hg38): 15:44554817-44663688

Previous symbols: [ "KIAA1840", "ALS5" ]

Links

ENSG00000104133 ∙ NCBI:80208 ∙ OMIM:610844 ∙ HGNC:11226 ∙ Uniprot:Q96JI7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary spastic paraplegia 11 (Definitive), mode of inheritance: AR
• hereditary spastic paraplegia 11 (Strong), mode of inheritance: AR
• Charcot-Marie-Tooth disease axonal type 2X (Strong), mode of inheritance: AR
• amyotrophic lateral sclerosis type 5 (Strong), mode of inheritance: AR
• hereditary spastic paraplegia 11 (Definitive), mode of inheritance: AR
• hereditary spastic paraplegia 11 (Supportive), mode of inheritance: AR
• juvenile amyotrophic lateral sclerosis (Supportive), mode of inheritance: AR
• Charcot-Marie-Tooth disease axonal type 2X (Supportive), mode of inheritance: AR
• amyotrophic lateral sclerosis type 5 (Strong), mode of inheritance: AR
• Charcot-Marie-Tooth disease axonal type 2X (Strong), mode of inheritance: AR
• hereditary spastic paraplegia 11 (Strong), mode of inheritance: AR
• hereditary spastic paraplegia 11 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Amyotrophic lateral sclerosis 5, juvenile recessive; Charcot-Marie-Tooth disease, axonal, type 2X; Spastic paraplegia 11, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	17717710; 18067136; 17322883; 18663179; 18787847; 19196735; 19194956; 19513778; 20108361; 20110243; 20301389; 20390432; 20571989; 20971220; 21035867; 21381113; 21625935; 22154821; 22175763; 23043354; 23121729; 26556829

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPG11 gene.

• Hereditary spastic paraplegia 11 (2412 variants)
• not provided (470 variants)
• Inborn genetic diseases (392 variants)
• Amyotrophic lateral sclerosis type 5 (211 variants)
• Charcot-Marie-Tooth disease axonal type 2X (203 variants)
• Hereditary spastic paraplegia (141 variants)
• not specified (73 variants)
• Amyotrophic lateral sclerosis type 5;Hereditary spastic paraplegia 11;Charcot-Marie-Tooth disease axonal type 2X (12 variants)
• Amyotrophic lateral sclerosis type 5;Charcot-Marie-Tooth disease axonal type 2X;Hereditary spastic paraplegia 11 (12 variants)
• Amyotrophic lateral sclerosis (10 variants)
• SPG11-related condition (10 variants)
• Spastic Paraplegia, Recessive (7 variants)
• Abnormal central motor function (7 variants)
• Hereditary spastic paraplegia 11;Amyotrophic lateral sclerosis type 5;Charcot-Marie-Tooth disease axonal type 2X (5 variants)
• Hereditary spastic paraplegia 11;Charcot-Marie-Tooth disease axonal type 2X;Amyotrophic lateral sclerosis type 5 (4 variants)
• See cases (3 variants)
• Intellectual disability (3 variants)
• Charcot-Marie-Tooth disease axonal type 2X;Amyotrophic lateral sclerosis type 5;Hereditary spastic paraplegia 11 (3 variants)
• Hereditary spastic paraplegia 11;Charcot-Marie-Tooth disease axonal type 2X;Juvenile amyotrophic lateral sclerosis (2 variants)
• SPG11-related spastic paraplegia (2 variants)
• Spastic paraplegia (2 variants)
• Spastic paraparesis;Generalized hyperreflexia;Gait disturbance;Difficulty walking (2 variants)
• Amyotrophic lateral sclerosis type 5;Hereditary spastic paraplegia 11 (2 variants)
• Abnormal brain morphology (1 variants)
• Hereditary spastic paraplegia 11;Amyotrophic lateral sclerosis type 5 (1 variants)
• Juvenile amyotrophic lateral sclerosis;Hereditary spastic paraplegia 11;Charcot-Marie-Tooth disease axonal type 2X (1 variants)
• Spastic ataxia (1 variants)
• Charcot-Marie-Tooth disease axonal type 2X;Hereditary spastic paraplegia 11;Amyotrophic lateral sclerosis type 5 (1 variants)
• Early-onset Parkinson disease 20 (1 variants)
• Charcot-Marie-Tooth disease axonal type 2X;Hereditary spastic paraplegia 11 (1 variants)
• Hereditary spastic paraplegia 11;Juvenile amyotrophic lateral sclerosis;Charcot-Marie-Tooth disease axonal type 2X (1 variants)
• Charcot-Marie-Tooth disease axonal type 2X;Hereditary spastic paraplegia 11;Juvenile amyotrophic lateral sclerosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPG11 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			21	481	5	507
missense	2	7	1133	30	2	1174
nonsense	88	21	4			113
start loss			1			1
frameshift	155	31	8			194
inframe indel	1		22	1		24
splice donor/acceptor (+/-2bp)	20	38	4			62
splice region	2	4	62	96	1	165
non coding		2	18	267	44	331
Total	266	99	1211	779	51

Highest pathogenic variant AF is 0.0000591

Variants in SPG11

This is a list of pathogenic ClinVar variants found in the SPG11 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-44557613-T-A		not specified	Uncertain significance (Feb 13, 2024)
15-44562722-A-AAAGAT		Spastic Paraplegia, Recessive	Uncertain significance (Jun 14, 2016)
15-44562733-T-G		Hereditary spastic paraplegia 11	Uncertain significance (Jan 13, 2018)
15-44562749-G-GTATC		Spastic Paraplegia, Recessive	Uncertain significance (Jun 14, 2016)
15-44562801-G-A		Spastic Paraplegia, Recessive	Uncertain significance (Jun 14, 2016)
15-44562822-C-A		Hereditary spastic paraplegia 11	Uncertain significance (Jan 13, 2018)
15-44562878-T-C		Hereditary spastic paraplegia 11 • Amyotrophic lateral sclerosis type 5 • Charcot-Marie-Tooth disease axonal type 2X	Likely benign (Oct 10, 2019)
15-44562880-G-C		Hereditary spastic paraplegia 11	Uncertain significance (Jan 12, 2018)
15-44563118-C-T		SPG11-related disorder	Likely benign (Mar 08, 2019)
15-44563124-ACCTGCTAG-A		Hereditary spastic paraplegia 11	Uncertain significance (May 22, 2022)
15-44563126-CT-C		Hereditary spastic paraplegia 11 • Inborn genetic diseases • Amyotrophic lateral sclerosis type 5;Charcot-Marie-Tooth disease axonal type 2X;Hereditary spastic paraplegia 11	Uncertain significance (Nov 19, 2021)
15-44563128-G-A		Hereditary spastic paraplegia 11	Uncertain significance (Nov 24, 2021)
15-44563129-C-G		Hereditary spastic paraplegia 11 • Amyotrophic lateral sclerosis type 5;Hereditary spastic paraplegia 11;Charcot-Marie-Tooth disease axonal type 2X	Uncertain significance (May 03, 2022)
15-44563129-C-T		Hereditary spastic paraplegia 11	Uncertain significance (Oct 26, 2022)
15-44563131-A-G		Hereditary spastic paraplegia 11	Uncertain significance (Aug 31, 2021)
15-44563132-G-T			Uncertain significance (May 01, 2022)
15-44563133-C-T		Hereditary spastic paraplegia 11	Uncertain significance (Aug 27, 2021)
15-44563135-T-G		Hereditary spastic paraplegia 11	Uncertain significance (Oct 25, 2020)
15-44563136-G-A		Hereditary spastic paraplegia	Uncertain significance (Dec 12, 2016)
15-44563140-T-C		Hereditary spastic paraplegia 11	Uncertain significance (Apr 07, 2022)
15-44563142-T-C		Hereditary spastic paraplegia 11	Likely benign (Aug 10, 2023)
15-44563146-C-T		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
15-44563151-A-C		Hereditary spastic paraplegia 11	Likely benign (Aug 15, 2022)
15-44563151-A-G		Hereditary spastic paraplegia 11	Likely benign (Jan 24, 2024)
15-44563152-C-G		Hereditary spastic paraplegia 11 • Inborn genetic diseases	Uncertain significance (Jan 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPG11	protein_coding	protein_coding	ENST00000261866	40	100983

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.60e-39	0.947	125367	0	381	125748	0.00152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.39	1360	1.22e+3	1.11	0.0000609	16162
Missense in Polyphen		429	412.9	1.039		5520
Synonymous	-2.17	521	462	1.13	0.0000228	4514
Loss of Function	3.30	81	120	0.675	0.00000584	1505

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00264	0.00258
Ashkenazi Jewish	0.000993	0.000993
East Asian	0.00158	0.00158
Finnish	0.000647	0.000647
European (Non-Finnish)	0.00186	0.00186
Middle Eastern	0.00158	0.00158
South Asian	0.00151	0.00150
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in neurite plasticity by maintaining cytoskeleton stability and regulating synaptic vesicle transport. {ECO:0000269|PubMed:24794856}.
• Disease: DISEASE: Amyotrophic lateral sclerosis 5, juvenile (ALS5) [MIM:602099]: A form of amyotrophic lateral sclerosis, a neurodegenerative disorder affecting upper motor neurons in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be multifactorial, involving both genetic and environmental factors. The disease is inherited in 5- 10% of the cases. ALS5 is an autosomal recessive, juvenile form characterized by onset of upper and lower motor neuron signs before age 25. {ECO:0000269|PubMed:20110243}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Charcot-Marie-Tooth disease 2X (CMT2X) [MIM:616668]: An autosomal recessive, axonal form of Charcot-Marie-Tooth disease, a disorder of the peripheral nervous system, characterized by progressive weakness and atrophy, initially of the peroneal muscles and later of the distal muscles of the arms. Charcot- Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathies (designated CMT1 when they are dominantly inherited) and primary peripheral axonal neuropathies (CMT2). Neuropathies of the CMT2 group are characterized by signs of axonal degeneration in the absence of obvious myelin alterations, normal or slightly reduced nerve conduction velocities, and progressive distal muscle weakness and atrophy. CMT2X patients manifest a slowly progressive, peripheral neuropathy affecting the lower limbs and resulting in gait difficulties and distal sensory impairment. Some patients also have upper limb involvement. {ECO:0000269|PubMed:26556829}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.615
• rvis_EVS: -0.48
• rvis_percentile_EVS: 22.79

Haploinsufficiency Scores

• pHI: 0.483
• hipred: N
• hipred_score: 0.414
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.414

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Spg11
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: spg11
• Affected structure: retinal ganglion cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: chemical synaptic transmission;axo-dendritic transport;synaptic vesicle transport;axon extension;phagosome-lysosome fusion involved in apoptotic cell clearance;walking behavior
• Cellular component: nucleolus;cytoplasm;lysosomal membrane;cytosol;plasma membrane;axon;dendrite;cytoplasmic vesicle;synapse
• Molecular function: protein binding