GeneBe

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

  • neurodevelopmental disorder (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEPHS1 gene.

  • not_specified (27 variants)
  • not_provided (17 variants)
  • VERVERI-BRADY_SYNDROME_2 (3 variants)
  • SEPHS1-related_disorder (1 variants)
  • SEPHS1-related_developmental_delay (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. These statistics are base on transcript: NM_000012247.5. 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.

EffectPLPVUSLBBSum
synonymous
3
clinvar
 3
missense
2
clinvar
2
clinvar
35
clinvar
 39
nonsense
0
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
0
Total 2 2 36 3 0

Highest pathogenic variant AF is 0.0000065717704

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEPHS1protein_codingprotein_codingENST00000327347 830874
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.9760.0236125743021257450.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.24992400.4120.00001392583
Missense in Polyphen2070.6610.28304779
Synonymous-0.78110797.21.100.00000686763
Loss of Function3.46115.90.06296.76e-7190

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00001770.0000176
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

loftool
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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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