SELENOI

selenoprotein I, the group of Selenoproteins

Basic information

Region (hg38): 2:26308547-26395885

Previous symbols: [ "EPT1" ]

Links

ENSG00000138018 ∙ NCBI:85465 ∙ OMIM:607915 ∙ HGNC:29361 ∙ Uniprot:Q9C0D9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spastic paraplegia 81, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic; Ophthalmologic	28052917; 29500230

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SELENOI 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				4	3	7
missense			16		1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					9	9
Total	0	0	16	4	13

Variants in SELENOI

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

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

Position	Type	Phenotype	Significance	ClinVar
2-26309979-G-A		not specified	Uncertain significance (Sep 11, 2024)
2-26310050-A-G		not specified	Uncertain significance (Sep 26, 2023)
2-26310074-C-T		not specified	Likely benign (Jun 24, 2022)
2-26310084-G-A		not specified	Uncertain significance (Aug 19, 2024)
2-26310090-G-A		not specified	Uncertain significance (Dec 08, 2021)
2-26310718-T-C		not specified	Uncertain significance (Apr 04, 2024)
2-26310730-C-G		not specified	Uncertain significance (Sep 16, 2022)
2-26310732-G-A		not specified	Uncertain significance (Oct 04, 2024)
2-26310817-C-T		not specified	Uncertain significance (Nov 06, 2023)
2-26310844-C-T		not specified	Uncertain significance (Dec 09, 2024)
2-26310850-G-C		not specified	Uncertain significance (Oct 31, 2023)
2-26310889-C-T		not specified	Uncertain significance (Apr 18, 2024)
2-26310913-C-T		not specified	Uncertain significance (Oct 10, 2023)
2-26310937-C-G		not specified	Uncertain significance (Jul 13, 2022)
2-26310988-C-T		not specified	Uncertain significance (Dec 27, 2023)
2-26311018-G-C		not specified	Uncertain significance (Dec 15, 2022)
2-26311030-C-T			Likely benign (Apr 01, 2023)
2-26311086-C-T		not specified	Uncertain significance (Mar 01, 2024)
2-26311117-G-A		not specified	Uncertain significance (Feb 07, 2023)
2-26311194-G-T		not specified	Uncertain significance (Aug 26, 2024)
2-26311219-G-A			Benign (Sep 01, 2022)
2-26311224-C-T		not specified	Uncertain significance (Aug 19, 2024)
2-26311233-A-T		not specified	Uncertain significance (Oct 21, 2024)
2-26311258-T-C		not specified	Uncertain significance (Aug 01, 2024)
2-26311287-T-A		not specified	Uncertain significance (Sep 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SELENOI	protein_coding	protein_coding	ENST00000260585	10	87345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.642	0.358	124629	0	8	124637	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	131	197	0.665	0.00000938	2556
Missense in Polyphen		36	79.3	0.45397		1079
Synonymous	-0.0981	77	75.9	1.01	0.00000389	768
Loss of Function	3.41	4	20.8	0.193	9.68e-7	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000184
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000469	0.0000464
European (Non-Finnish)	0.0000183	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes phosphatidylethanolamine biosynthesis from CDP-ethanolamine. It thereby plays a central role in the formation and maintenance of vesicular membranes. Involved in the formation of phosphatidylethanolamine via 'Kennedy' pathway.
• Pathway: Ether lipid metabolism - Homo sapiens (human);Glycerophospholipid metabolism - Homo sapiens (human);Phosphonate and phosphinate metabolism - Homo sapiens (human);Selenium Micronutrient Network;Selenium Metabolism and Selenoproteins;Metabolism of lipids;Metabolism;Synthesis of PE;phosphatidylethanolamine biosynthesis II;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Intolerance Scores

• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.786
• ghis: 0.578

Essentials

• essential_gene_gene_trap: K

Mouse Genome Informatics

• Gene name: Selenoi

Gene ontology

• Biological process: phosphatidylethanolamine biosynthetic process
• Cellular component: endoplasmic reticulum membrane;Golgi apparatus;integral component of membrane
• Molecular function: ethanolaminephosphotransferase activity;phosphotransferase activity, for other substituted phosphate groups;metal ion binding