SECISBP2L

SECIS binding protein 2 like

Basic information

Region (hg38): 15:48988476-49046447

Links

ENSG00000138593 ∙ NCBI:9728 ∙ OMIM:615756 ∙ HGNC:28997 ∙ Uniprot:Q93073 ∙ 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 SECISBP2L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SECISBP2L 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				2	1	3
missense			50	2		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	52	4	1

Variants in SECISBP2L

This is a list of pathogenic ClinVar variants found in the SECISBP2L region.

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

Position	Type	Phenotype	Significance	ClinVar
15-48992249-T-C		not specified	Uncertain significance (Feb 28, 2023)
15-48992257-G-A		not specified	Uncertain significance (Apr 12, 2022)
15-48992287-T-C		not specified	Likely benign (Sep 14, 2022)
15-48992333-G-C		not specified	Uncertain significance (Mar 20, 2024)
15-48992383-G-A		not specified	Uncertain significance (Feb 21, 2024)
15-48992407-C-T		not specified	Uncertain significance (Oct 06, 2021)
15-48992419-T-C		not specified	Uncertain significance (Dec 22, 2023)
15-48992484-T-A			Likely benign (Mar 01, 2024)
15-48992546-A-C		not specified	Uncertain significance (Apr 01, 2024)
15-48992561-C-T		not specified	Uncertain significance (Sep 16, 2021)
15-48992644-C-T		not specified	Uncertain significance (Nov 18, 2022)
15-48992732-C-T		not specified	Uncertain significance (Dec 08, 2023)
15-48992738-A-C		not specified	Uncertain significance (Mar 15, 2024)
15-48992753-T-C		not specified	Uncertain significance (Nov 15, 2021)
15-48992756-C-A		not specified	Uncertain significance (May 28, 2024)
15-48992926-T-C		not specified	Uncertain significance (Dec 11, 2023)
15-48996449-A-T			Likely benign (May 21, 2018)
15-48996462-T-C		not specified	Uncertain significance (Jan 23, 2024)
15-48996520-C-T		not specified	Uncertain significance (Dec 15, 2022)
15-48996530-A-G			Benign (May 21, 2018)
15-49000920-C-G		not specified	Uncertain significance (Oct 06, 2021)
15-49001029-C-G		not specified	Uncertain significance (Aug 21, 2023)
15-49009318-T-C		not specified	Uncertain significance (Jun 29, 2022)
15-49009358-T-C		not specified	Uncertain significance (Oct 25, 2022)
15-49011761-C-T		not specified	Uncertain significance (Nov 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SECISBP2L	protein_coding	protein_coding	ENST00000559471	18	58088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.285	0.715	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	455	557	0.817	0.0000271	7246
Missense in Polyphen		149	241.77	0.6163		2984
Synonymous	-0.186	196	193	1.02	0.00000943	2078
Loss of Function	5.14	12	52.0	0.231	0.00000278	654

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000370	0.000370
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000163	0.000163
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds SECIS (Sec insertion sequence) elements present on selenocysteine (Sec) protein mRNAs, but does not promote Sec incorporation into selenoproteins in vitro.

Intolerance Scores

• loftool: 0.242
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.68

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.466
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.141

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Secisbp2l

Gene ontology

• Biological process: selenocysteine incorporation
• Cellular component: ribonucleoprotein complex
• Molecular function: RNA binding;mRNA 3'-UTR binding;protein binding;selenocysteine insertion sequence binding;ribonucleoprotein complex binding