SP140L

SP140 nuclear body protein like, the group of Bromodomain containing|PHD finger proteins

Basic information

Region (hg38): 2:230327184-230403732

Links

ENSG00000185404 ∙ NCBI:93349 ∙ OMIM:617747 ∙ HGNC:25105 ∙ Uniprot:Q9H930 ∙ 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 SP140L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SP140L 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				1		1
missense			23	6		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	24	7	0

Variants in SP140L

This is a list of pathogenic ClinVar variants found in the SP140L region.

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

Position	Type	Phenotype	Significance	ClinVar
2-230327288-G-C		not specified	Uncertain significance (Aug 22, 2023)
2-230357809-T-C		not specified	Uncertain significance (Apr 06, 2022)
2-230357862-G-T		not specified	Uncertain significance (Jul 16, 2024)
2-230357914-C-T		not specified	Uncertain significance (Apr 24, 2024)
2-230357932-C-T		not specified	Uncertain significance (Dec 19, 2023)
2-230357933-G-A		not specified	Uncertain significance (Oct 20, 2024)
2-230357935-G-A		not specified	Uncertain significance (Dec 03, 2024)
2-230357938-C-T		not specified	Uncertain significance (Oct 17, 2024)
2-230358974-A-T		not specified	Uncertain significance (Feb 15, 2023)
2-230359006-G-A		not specified	Uncertain significance (Aug 19, 2024)
2-230359097-C-G		not specified	Uncertain significance (Feb 17, 2022)
2-230361622-G-T		not specified	Uncertain significance (Sep 06, 2022)
2-230370908-G-A		not specified	Likely benign (Dec 28, 2022)
2-230370926-C-T		not specified	Uncertain significance (Nov 03, 2022)
2-230370936-G-C		not specified	Uncertain significance (Nov 23, 2024)
2-230370949-C-A		not specified	Uncertain significance (Jan 29, 2024)
2-230371604-T-C		not specified	Uncertain significance (Nov 20, 2024)
2-230371612-G-A		not specified	Uncertain significance (Feb 27, 2023)
2-230371630-G-A		not specified	Uncertain significance (Aug 02, 2022)
2-230383552-C-T		not specified	Uncertain significance (Sep 13, 2023)
2-230385224-A-G		not specified	Uncertain significance (Apr 30, 2024)
2-230385263-A-G		not specified	Uncertain significance (Aug 23, 2021)
2-230385274-A-G		not specified	Likely benign (May 10, 2022)
2-230385302-G-C		not specified	Uncertain significance (Nov 05, 2021)
2-230388595-A-G		not specified	Uncertain significance (May 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SP140L	protein_coding	protein_coding	ENST00000415673	19	76549

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.79e-9	0.993	125659	0	89	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0868	297	293	1.01	0.0000149	3845
Missense in Polyphen		92	94.135	0.97732		1317
Synonymous	-0.783	117	107	1.10	0.00000595	975
Loss of Function	2.51	19	35.1	0.542	0.00000171	462

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00332	0.00324
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000255	0.000246
Middle Eastern	0.00	0.00
South Asian	0.000103	0.0000980
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.621
• rvis_EVS: 1.44
• rvis_percentile_EVS: 95.09

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.214
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sp140

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nuclear body
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding