SEPHS1

selenophosphate synthetase 1

Basic information

Region (hg38): 10:13317428-13348298

Links

ENSG00000086475 ∙ NCBI:22929 ∙ OMIM:600902 ∙ HGNC:19685 ∙ Uniprot:P49903 ∙ 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 SEPHS1 gene.

• not provided (3 variants)
• SEPHS1-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEPHS1 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	3	1	22			26
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	3	1	23	0	1

Highest pathogenic variant AF is 0.00000657

Variants in SEPHS1

This is a list of pathogenic ClinVar variants found in the SEPHS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-13319203-A-G		not specified	Uncertain significance (Apr 23, 2024)
10-13319209-C-T			Pathogenic (Feb 24, 2022)
10-13319210-G-A		SEPHS1-related disorder	Pathogenic (Feb 24, 2022)
10-13319210-G-C			Likely pathogenic (Jun 30, 2022)
10-13319267-A-C			Pathogenic (Feb 24, 2022)
10-13319298-C-CT			Uncertain significance (Mar 25, 2023)
10-13319332-C-T			Uncertain significance (May 09, 2022)
10-13319333-G-A			Uncertain significance (Dec 10, 2022)
10-13322852-G-C		not specified	Uncertain significance (May 12, 2024)
10-13322868-C-T		not specified	Uncertain significance (Aug 10, 2021)
10-13322975-G-C		not specified	Uncertain significance (Jun 16, 2023)
10-13322991-C-T			Uncertain significance (Apr 27, 2023)
10-13323024-T-A		not specified	Uncertain significance (Oct 03, 2022)
10-13323028-C-G			Likely benign (Mar 01, 2025)
10-13328378-T-G		not specified	Uncertain significance (Jan 17, 2025)
10-13328429-T-C		not specified	Uncertain significance (Dec 03, 2024)
10-13329705-A-T		not specified	Uncertain significance (Nov 17, 2023)
10-13329744-G-A		not specified	Uncertain significance (Dec 20, 2023)
10-13333829-T-C		not specified	Uncertain significance (May 03, 2023)
10-13333902-C-T		not specified	Uncertain significance (Sep 14, 2022)
10-13333906-T-C			Benign (Apr 16, 2020)
10-13333923-C-T			Uncertain significance (Jan 04, 2022)
10-13333926-C-T		not specified	Uncertain significance (Jan 26, 2022)
10-13333927-G-A			Likely benign (Jan 01, 2025)
10-13333952-G-A		not specified	Uncertain significance (Aug 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEPHS1	protein_coding	protein_coding	ENST00000327347	8	30874

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.976	0.0236	125743	0	2	125745	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.24	99	240	0.412	0.0000139	2583
Missense in Polyphen		20	70.661	0.28304		779
Synonymous	-0.781	107	97.2	1.10	0.00000686	763
Loss of Function	3.46	1	15.9	0.0629	6.76e-7	190

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)	0.0000177	0.0000176
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. {ECO:0000269|PubMed:7665581}.
• Pathway: Selenocompound metabolism - Homo sapiens (human);selenocysteine biosynthesis (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• rvis_EVS: -0.65
• rvis_percentile_EVS: 16.36

Haploinsufficiency Scores

• pHI: 0.691
• hipred: Y
• hipred_score: 0.662
• ghis: 0.709

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.990

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sephs1
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; embryo phenotype; liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: selenium compound metabolic process;cellular protein modification process;selenocysteine biosynthetic process;phosphorylation;tRNA seleno-modification
• Cellular component: cytoplasm;plasma membrane;nuclear membrane
• Molecular function: selenide, water dikinase activity;protein binding;ATP binding;GTP binding;identical protein binding