SPART-AS1

SPART antisense RNA 1, the group of Antisense RNAs

Basic information

Region (hg38): 13:36346431-36369601

Previous symbols: [ "C13orf43", "SPG20OS", "SPG20-AS1" ]

Links

ENSG00000120664 ∙ NCBI:100507135 ∙ ∙ HGNC:39933 ∙ Uniprot:P0CW21 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPART-AS1 gene.

• Troyer syndrome (3 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPART-AS1 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						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2	1	1	4
Total	0	0	2	1	1

Variants in SPART-AS1

This is a list of pathogenic ClinVar variants found in the SPART-AS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-36346467-CCA-C		Troyer syndrome	Uncertain significance (Jun 14, 2016)
13-36346475-C-T		Troyer syndrome	Benign/Likely benign (Mar 28, 2022)
13-36346483-A-C		Troyer syndrome	Uncertain significance (Jun 14, 2016)
13-36346781-C-G			Benign (Mar 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPART-AS1	protein_coding	protein_coding	ENST00000379848	3	23171

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0237	0.562	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.145	12	13.5	0.889	6.57e-7	340
Missense in Polyphen		3	2.7349	1.0969		79
Synonymous	-0.124	4	3.70	1.08	1.60e-7	81
Loss of Function	-0.0666	2	1.90	1.05	1.19e-7	30

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• ghis: 0.518