SEPHS2

selenophosphate synthetase 2, the group of Selenoproteins

Basic information

Region (hg38): 16:30443630-30445874

Links

ENSG00000179918 ∙ NCBI:22928 ∙ OMIM:606218 ∙ HGNC:19686 ∙ Uniprot:Q99611 ∙ 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 SEPHS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPHS2 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	1		19
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	1	0

Variants in SEPHS2

This is a list of pathogenic ClinVar variants found in the SEPHS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30444407-T-C		not specified	Uncertain significance (Nov 08, 2022)
16-30444428-C-T		not specified	Uncertain significance (Sep 20, 2023)
16-30444460-A-G		not specified	Uncertain significance (Dec 21, 2022)
16-30444629-A-G		not specified	Uncertain significance (Feb 06, 2023)
16-30444671-C-T		not specified	Likely benign (Feb 06, 2023)
16-30444710-C-A		not specified	Uncertain significance (Mar 01, 2023)
16-30444727-C-T		not specified	Uncertain significance (Dec 20, 2023)
16-30444737-T-C		not specified	Uncertain significance (May 15, 2023)
16-30444997-A-G		not specified	Uncertain significance (Dec 15, 2022)
16-30445105-G-C		not specified	Uncertain significance (May 10, 2024)
16-30445129-C-T		not specified	Uncertain significance (Jun 13, 2023)
16-30445136-C-T		not specified	Uncertain significance (Jun 10, 2024)
16-30445142-C-A		not specified	Uncertain significance (Dec 08, 2023)
16-30445304-G-A		not specified	Uncertain significance (Jun 29, 2023)
16-30445378-A-C		not specified	Uncertain significance (Apr 15, 2024)
16-30445387-G-A		not specified	Uncertain significance (Apr 09, 2024)
16-30445402-C-T		not specified	Uncertain significance (Aug 04, 2021)
16-30445408-C-G		not specified	Uncertain significance (May 30, 2024)
16-30445420-G-C		not specified	Uncertain significance (Feb 05, 2024)
16-30445559-T-C		not specified	Uncertain significance (Aug 17, 2021)
16-30445640-G-A		not specified	Uncertain significance (Feb 28, 2024)
16-30445640-G-C		not specified	Uncertain significance (Mar 31, 2024)
16-30445675-T-C		not specified	Uncertain significance (Jun 05, 2023)
16-30445700-A-G		not specified	Uncertain significance (Feb 16, 2023)
16-30445724-C-T		not specified	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEPHS2	protein_coding	protein_coding	ENST00000500504	1	2551

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00222	0.927	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.76	184	265	0.695	0.0000147	2860
Missense in Polyphen		44	78.178	0.56282		893
Synonymous	1.51	94	115	0.820	0.00000724	975
Loss of Function	1.58	6	11.9	0.505	6.75e-7	130

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Synthesizes selenophosphate from selenide and ATP.
• Pathway: Selenocompound metabolism - Homo sapiens (human);Selenoamino Acid Metabolism;Selenium Micronutrient Network;Selenium Metabolism and Selenoproteins;Selenocysteine synthesis;Metabolism of amino acids and derivatives;selenocysteine biosynthesis;Metabolism;Selenoamino acid metabolism (Consensus)

Intolerance Scores

• loftool: 0.670
• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.51

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.309

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.401

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sephs2

Gene ontology

• Biological process: selenium compound metabolic process;selenocysteine metabolic process;selenocysteine biosynthetic process;phosphorylation;tRNA seleno-modification
• Cellular component: cellular_component;cytoplasm;cytosol
• Molecular function: selenide, water dikinase activity;ATP binding