SECISBP2

SECIS binding protein 2

Basic information

Region (hg38): 9:89318500-89359663

Links

ENSG00000187742NCBI:79048OMIM:607693HGNC:30972Uniprot:Q96T21AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • thyroid hormone metabolism, abnormal 1 (Strong), mode of inheritance: AR
  • thyroid hormone metabolism, abnormal 1 (Strong), mode of inheritance: AR
  • short stature-delayed bone age due to thyroid hormone metabolism deficiency (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Selenoprotein deficiency; Thyroid hormone metabolism, abnormal, 1ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingAudiologic/Otolaryngologic; Endocrine; Musculoskeletal; Neurologic16228000; 19265499; 19602558; 19769464; 20501692; 20685891; 21084748; 21511232; 22247018; 22986150; 29882503
Findings, such as growth retardation, may be transient, and the overall phenotypic range has been described as wide

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SECISBP2 gene.

  • Inborn_genetic_diseases (102 variants)
  • not_provided (23 variants)
  • Thyroid_hormone_metabolism,_abnormal_1 (12 variants)
  • SECISBP2-related_disorder (11 variants)
  • not_specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SECISBP2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024077.5. 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
1
clinvar
11
clinvar
1
clinvar
13
missense
1
clinvar
103
clinvar
6
clinvar
3
clinvar
113
nonsense
3
clinvar
2
clinvar
1
clinvar
6
start loss
0
frameshift
2
clinvar
2
clinvar
4
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
3
Total 6 7 105 17 4

Highest pathogenic variant AF is 0.0000303591

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SECISBP2protein_codingprotein_codingENST00000375807 1741137
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.19e-180.17812556401841257480.000732
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.005204394390.9990.00002305580
Missense in Polyphen131134.640.972951780
Synonymous-2.232011651.220.000008721645
Loss of Function1.413342.90.7680.00000234546

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001800.00180
Ashkenazi Jewish0.0006950.000695
East Asian0.001090.00109
Finnish0.0004160.000416
European (Non-Finnish)0.0006000.000598
Middle Eastern0.001090.00109
South Asian0.0007190.000719
Other0.0008170.000815

dbNSFP

Source: dbNSFP

Function
FUNCTION: Binds to the SECIS element in the 3'-UTR of some mRNAs encoding selenoproteins. Binding is stimulated by SELB.;
Pathway
Selenocysteine synthesis;Metabolism of amino acids and derivatives;Metabolism;Selenoamino acid metabolism (Consensus)

Recessive Scores

pRec
0.0900

Intolerance Scores

loftool
0.878
rvis_EVS
-0.53
rvis_percentile_EVS
20.82

Haploinsufficiency Scores

pHI
0.0904
hipred
N
hipred_score
0.145
ghis
0.539

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.479

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Secisbp2
Phenotype
embryo phenotype; pigmentation phenotype; hematopoietic 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); vision/eye phenotype; limbs/digits/tail phenotype; skeleton phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype;

Gene ontology

Biological process
selenocysteine incorporation;striatum development;neuron development;negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
Cellular component
nucleus;mitochondrion;ribonucleoprotein complex
Molecular function
RNA binding;mRNA 3'-UTR binding;protein binding;selenocysteine insertion sequence binding;ribonucleoprotein complex binding