SPARCL1

SPARC like 1, the group of SPARC family

Basic information

Region (hg38): 4:87473334-87531061

Links

ENSG00000152583 ∙ NCBI:8404 ∙ OMIM:606041 ∙ HGNC:11220 ∙ Uniprot:Q14515 ∙ 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 SPARCL1 gene.

• Inborn genetic diseases (21 variants)
• SPARCL1-related condition (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPARCL1 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in SPARCL1

This is a list of pathogenic ClinVar variants found in the SPARCL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-87480385-G-A		not specified	Uncertain significance (Mar 11, 2024)
4-87480493-T-C		not specified	Uncertain significance (Jan 10, 2023)
4-87482465-A-T		not specified	Uncertain significance (Jun 27, 2022)
4-87482516-G-A		not specified	Uncertain significance (Dec 02, 2022)
4-87482558-T-C		not specified	Uncertain significance (May 31, 2023)
4-87490335-C-T		not specified	Uncertain significance (Feb 16, 2023)
4-87490342-T-A		not specified	Uncertain significance (May 27, 2022)
4-87490351-G-T		not specified	Uncertain significance (Jun 02, 2023)
4-87490377-T-C		not specified	Uncertain significance (Mar 23, 2022)
4-87493595-C-G		not specified	Uncertain significance (Mar 06, 2023)
4-87493595-C-T		not specified	Uncertain significance (Feb 27, 2024)
4-87493602-C-G		not specified	Uncertain significance (Apr 07, 2023)
4-87493670-A-G		not specified	Uncertain significance (May 17, 2023)
4-87493748-T-G		not specified	Uncertain significance (Mar 06, 2023)
4-87493755-C-T		not specified	Uncertain significance (Nov 21, 2022)
4-87493766-CCAT-C		SPARCL1-related disorder	Uncertain significance (Feb 09, 2023)
4-87493818-C-T		not specified	Uncertain significance (Apr 28, 2022)
4-87493829-G-A		SPARCL1-related disorder	Uncertain significance (Jan 11, 2023)
4-87493883-C-G		not specified	Uncertain significance (Jul 27, 2022)
4-87493909-C-A		not specified	Uncertain significance (Jul 27, 2022)
4-87493950-C-T		not specified	Likely benign (Aug 30, 2022)
4-87493985-G-T		not specified	Uncertain significance (Nov 09, 2023)
4-87494108-C-T		not specified	Uncertain significance (Dec 14, 2023)
4-87494175-C-A		SPARCL1-related disorder	Uncertain significance (Apr 27, 2023)
4-87494210-A-G		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPARCL1	protein_coding	protein_coding	ENST00000418378	10	57727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.64e-10	0.843	125709	0	38	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0639	337	340	0.990	0.0000162	4481
Missense in Polyphen		95	99.348	0.95624		1305
Synonymous	0.944	110	123	0.892	0.00000641	1127
Loss of Function	1.70	19	28.8	0.659	0.00000131	384

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000203	0.000203
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.00	0.00
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000151	0.000149
Middle Eastern	0.00	0.00
South Asian	0.000371	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Recessive Scores

• pRec: 0.0870

Intolerance Scores

• loftool: 0.456
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.3

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.123
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.331

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sparcl1
• 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)

Gene ontology

• Biological process: signal transduction;post-translational protein modification;cellular protein metabolic process;synaptic membrane adhesion
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;collagen-containing extracellular matrix;glutamatergic synapse
• Molecular function: calcium ion binding;protein binding;collagen binding;extracellular matrix binding