SPART

spartin

Basic information

Region (hg38): 13:36301637-36370180

Previous symbols: [ "SPG20" ]

Links

ENSG00000133104 ∙ NCBI:23111 ∙ OMIM:607111 ∙ HGNC:18514 ∙ Uniprot:Q8N0X7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Troyer syndrome (Supportive), mode of inheritance: AR
• Troyer syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spastic paraplegia 20, autosomal recessive (Troyer syndrome)	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	Craniofacial; Musculoskeletal; Neurologic	6022528; 12134148; 18413476; 20437587; 26003402

ClinVar

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

• not provided (222 variants)
• Troyer syndrome (100 variants)
• Hereditary spastic paraplegia (18 variants)
• not specified (8 variants)
• Inborn genetic diseases (8 variants)
• Neurodevelopmental delay (3 variants)
• SPART-related condition (2 variants)
• 6 conditions (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPART 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			5	49	1	55
missense			118	4		122
nonsense	3	2				5
start loss						0
frameshift	8	5	2			15
inframe indel			2			2
splice donor/acceptor (+/-2bp)			1			1
splice region			2			2
non coding			44	31	11	86
Total	11	7	172	84	12

Highest pathogenic variant AF is 0.0000394

Variants in SPART

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

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

Position	Type	Phenotype	Significance	ClinVar
13-36301648-G-T		Troyer syndrome	Uncertain significance (Jan 13, 2018)
13-36301909-A-G		Troyer syndrome	Uncertain significance (Jan 13, 2018)
13-36301911-T-A		Troyer syndrome	Uncertain significance (Jan 12, 2018)
13-36302022-A-G		Troyer syndrome	Likely benign (Apr 27, 2017)
13-36302066-A-G		Troyer syndrome	Uncertain significance (Jan 12, 2018)
13-36302085-A-G		Troyer syndrome	Uncertain significance (Jan 13, 2018)
13-36302109-C-T		Troyer syndrome	Uncertain significance (Jan 13, 2018)
13-36302161-G-A		Troyer syndrome	Uncertain significance (Jan 13, 2018)
13-36302210-ATACCT-A		Troyer syndrome	Uncertain significance (Jun 14, 2016)
13-36302234-TTATC-T		Troyer syndrome	Likely benign (Jun 14, 2016)
13-36302242-A-G		Troyer syndrome	Benign (Jan 13, 2018)
13-36302294-A-G		Troyer syndrome	Uncertain significance (Jan 12, 2018)
13-36302312-G-A		Troyer syndrome	Uncertain significance (Jan 12, 2018)
13-36302330-A-G		Troyer syndrome	Uncertain significance (Jan 12, 2018)
13-36302342-A-T		Troyer syndrome	Uncertain significance (Jan 12, 2018)
13-36302457-T-C		Troyer syndrome	Uncertain significance (Jan 13, 2018)
13-36302473-C-T		Troyer syndrome	Uncertain significance (Jan 12, 2018)
13-36302517-T-G		Troyer syndrome	Uncertain significance (Jan 13, 2018)
13-36302518-C-G		Troyer syndrome	Uncertain significance (Jan 12, 2018)
13-36302566-C-T		Troyer syndrome	Likely benign (Apr 27, 2017)
13-36302571-T-C		Troyer syndrome	Uncertain significance (Jan 12, 2018)
13-36302614-T-A		Troyer syndrome	Uncertain significance (Jan 13, 2018)
13-36302679-C-T		Troyer syndrome	Uncertain significance (Jan 13, 2018)
13-36302720-G-A		Troyer syndrome	Uncertain significance (Jan 15, 2018)
13-36302741-G-A		Troyer syndrome	Uncertain significance (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPART	protein_coding	protein_coding	ENST00000451493	8	68543

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.97e-7	0.983	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0699	346	350	0.989	0.0000181	4325
Missense in Polyphen		84	87.117	0.96423		1055
Synonymous	0.0128	130	130	0.999	0.00000719	1320
Loss of Function	2.22	15	27.5	0.545	0.00000132	355

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000597	0.000597
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000229	0.000229
Middle Eastern	0.000272	0.000272
South Asian	0.000359	0.000359
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be implicated in endosomal trafficking, or microtubule dynamics, or both. Participates in cytokinesis (PubMed:20719964). {ECO:0000269|PubMed:20719964}.
• Disease: DISEASE: Spastic paraplegia 20, autosomal recessive (SPG20) [MIM:275900]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. SPG20 is characterized by dysarthria, distal amyotrophy, mild developmental delay and short stature. {ECO:0000269|PubMed:12134148, ECO:0000269|PubMed:27539578, ECO:0000269|PubMed:28875386}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Endocytosis - Homo sapiens (human);EGFR1 (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.7

Haploinsufficiency Scores

• pHI: 0.167
• hipred: Y
• hipred_score: 0.752
• ghis: 0.591

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Spg20
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; skeleton 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); neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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)

Gene ontology

• Biological process: abscission;negative regulation of BMP signaling pathway;lipid droplet organization;negative regulation of collateral sprouting in absence of injury;neuromuscular process;cell division;regulation of mitochondrial membrane potential;adipose tissue development
• Cellular component: cytoplasm;mitochondrial outer membrane;lipid droplet;cytosol;plasma membrane;midbody;synapse
• Molecular function: protein binding;ubiquitin protein ligase binding