SPOPL

speckle type BTB/POZ protein like, the group of BTB domain containing

Basic information

Region (hg38): 2:138501770-138574458

Links

ENSG00000144228 ∙ NCBI:339745 ∙ ∙ HGNC:27934 ∙ Uniprot:Q6IQ16 ∙ 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 SPOPL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPOPL 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			18	3		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	3	0

Variants in SPOPL

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

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

Position	Type	Phenotype	Significance	ClinVar
2-138550278-G-C		not specified	Uncertain significance (Sep 02, 2024)
2-138550550-G-A		not specified	Uncertain significance (Sep 27, 2024)
2-138550922-A-G		not specified	Uncertain significance (Oct 12, 2024)
2-138550954-G-T		not specified	Uncertain significance (Nov 30, 2021)
2-138550964-T-G		not specified	Uncertain significance (Apr 06, 2023)
2-138551000-G-A		not specified	Uncertain significance (Dec 08, 2023)
2-138551027-G-C		not specified	Uncertain significance (Jul 13, 2021)
2-138551034-G-A		not specified	Uncertain significance (Jun 29, 2023)
2-138552627-G-T		not specified	Uncertain significance (Aug 22, 2022)
2-138552628-C-T		not specified	Uncertain significance (Aug 22, 2022)
2-138552663-G-C		not specified	Uncertain significance (Oct 06, 2024)
2-138552665-T-C		not specified	Uncertain significance (Nov 21, 2024)
2-138552672-A-C		not specified	Uncertain significance (May 25, 2022)
2-138559026-G-A		not specified	Uncertain significance (Jun 07, 2023)
2-138559050-T-C		not specified	Uncertain significance (Jul 09, 2024)
2-138559061-A-G		not specified	Uncertain significance (Aug 15, 2024)
2-138559190-G-A		not specified	Uncertain significance (Dec 03, 2024)
2-138559302-G-A		not specified	Uncertain significance (Nov 14, 2024)
2-138559303-C-T		not specified	Uncertain significance (Mar 08, 2024)
2-138559305-A-G		not specified	Uncertain significance (Dec 01, 2022)
2-138560809-G-A		not specified	Likely benign (Jul 05, 2022)
2-138560826-T-G		not specified	Likely benign (Dec 13, 2021)
2-138564755-T-G		not specified	Uncertain significance (Dec 22, 2023)
2-138564817-A-T		not specified	Uncertain significance (Aug 12, 2021)
2-138568937-C-A		not specified	Uncertain significance (Dec 09, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPOPL	protein_coding	protein_coding	ENST00000280098	10	71747

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0119	0.988	125727	0	17	125744	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.960	171	210	0.814	0.0000106	2602
Missense in Polyphen		54	77.692	0.69505		1016
Synonymous	0.155	66	67.6	0.976	0.00000324	699
Loss of Function	3.15	8	25.0	0.320	0.00000145	274

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.0000927	0.0000924
European (Non-Finnish)	0.0000627	0.0000615
Middle Eastern	0.000218	0.000217
South Asian	0.000139	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of a cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins, but with relatively low efficiency. Cullin-RING-based BCR (BTB-CUL3- RBX1) E3 ubiquitin-protein ligase complexes containing homodimeric SPOPL or the heterodimer formed by SPOP and SPOPL are less efficient than ubiquitin ligase complexes containing only SPOP. May function to down-regulate the activity of cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complexes that contain SPOP. {ECO:0000269|PubMed:22632832}.
• Pathway: Hedgehog signaling pathway - Homo sapiens (human);Hedgehog Signaling Pathway;Signal Transduction;Hedgehog ,on, state;Signaling by Hedgehog (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.483
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.325
• hipred: N
• hipred_score: 0.492
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.635

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spopl
• Phenotype: normal phenotype; skeleton phenotype

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;regulation of proteolysis;negative regulation of protein ubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process
• Cellular component: nucleus;cytoplasm;Cul3-RING ubiquitin ligase complex
• Molecular function: protein binding;ubiquitin protein ligase binding