SECISBP2

SECIS binding protein 2

Basic information

Region (hg38): 9:89318499-89359663

Links

ENSG00000187742 ∙ NCBI:79048 ∙ OMIM:607693 ∙ HGNC:30972 ∙ Uniprot:Q96T21 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Selenoprotein deficiency; Thyroid hormone metabolism, abnormal, 1	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	Audiologic/Otolaryngologic; Endocrine; Musculoskeletal; Neurologic	16228000; 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 (35 variants)
• not provided (15 variants)
• Thyroid hormone metabolism, abnormal 1 (8 variants)
• SECISBP2-related condition (2 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.

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				4	1	5
missense			36	4	3	43
nonsense	2	1	1			4
start loss						0
frameshift	1	1				2
inframe indel						0
splice donor/acceptor (+/-2bp)	1	2				3
splice region			1	1	1	3
non coding						0
Total	4	4	37	8	4

Highest pathogenic variant AF is 0.0000723

Variants in SECISBP2

This is a list of pathogenic ClinVar variants found in the SECISBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-89318595-C-T		Inborn genetic diseases	Uncertain significance (Feb 17, 2022)
9-89319668-C-T		Inborn genetic diseases	Uncertain significance (Apr 26, 2023)
9-89319734-C-A		Inborn genetic diseases	Uncertain significance (Mar 31, 2023)
9-89319745-C-T		Inborn genetic diseases	Uncertain significance (Dec 31, 2023)
9-89319752-C-G		Thyroid hormone metabolism, abnormal 1	Uncertain significance (Apr 05, 2019)
9-89319752-C-T		Inborn genetic diseases	Uncertain significance (Nov 21, 2023)
9-89319775-G-T		Inborn genetic diseases	Uncertain significance (Apr 07, 2022)
9-89319798-G-A		Thyroid hormone metabolism, abnormal 1	Likely pathogenic (Jun 19, 2020)
9-89319800-A-T		SECISBP2-related disorder	Uncertain significance (Oct 12, 2022)
9-89325513-A-G		Inborn genetic diseases	Uncertain significance (Jun 29, 2022)
9-89325525-CT-C			Likely pathogenic (Oct 18, 2017)
9-89325570-C-G		Inborn genetic diseases	Uncertain significance (May 08, 2023)
9-89325591-C-A		Inborn genetic diseases	Uncertain significance (Jul 06, 2022)
9-89325602-C-T		Thyroid hormone metabolism, abnormal 1	Pathogenic (Nov 07, 2019)
9-89325603-G-A		Inborn genetic diseases	Uncertain significance (Jan 03, 2024)
9-89325666-C-T			Benign (Dec 31, 2019)
9-89325907-A-G		Inborn genetic diseases	Uncertain significance (Jan 24, 2023)
9-89325997-C-T		Inborn genetic diseases	Uncertain significance (Nov 21, 2022)
9-89326028-T-C		SECISBP2-related disorder	Likely benign (Feb 18, 2019)
9-89328674-C-T			Likely pathogenic (Oct 18, 2017)
9-89328699-T-C		Inborn genetic diseases	Uncertain significance (Apr 20, 2023)
9-89328710-G-T		Inborn genetic diseases	Uncertain significance (Feb 10, 2022)
9-89328780-A-G			Uncertain significance (-)
9-89328784-G-A			Likely benign (Mar 30, 2018)
9-89328795-A-T		Inborn genetic diseases	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SECISBP2	protein_coding	protein_coding	ENST00000375807	17	41137

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.19e-18	0.178	125564	0	184	125748	0.000732

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00520	439	439	0.999	0.0000230	5580
Missense in Polyphen		131	134.64	0.97295		1780
Synonymous	-2.23	201	165	1.22	0.00000872	1645
Loss of Function	1.41	33	42.9	0.768	0.00000234	546

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00180	0.00180
Ashkenazi Jewish	0.000695	0.000695
East Asian	0.00109	0.00109
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000600	0.000598
Middle Eastern	0.00109	0.00109
South Asian	0.000719	0.000719
Other	0.000817	0.000815

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

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

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