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

• spastic paraplegia 81, autosomal recessive (Strong), mode of inheritance: AR

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.

• not_specified (32 variants)
• not_provided (7 variants)
• Spastic_paraplegia_81,_autosomal_recessive (7 variants)
• SELENOI-related_condition (1 variants)

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. These statistics are base on transcript: NM_000033505.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous	1			4	1	6
missense	2		30	3		35
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)	1					1
Total	4	0	30	7	1

Highest pathogenic variant AF is 0.0000050425374

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