SPIB

Spi-B transcription factor, the group of ETS transcription factor family

Basic information

Region (hg38): 19:50418937-50431314

Links

ENSG00000269404 ∙ NCBI:6689 ∙ OMIM:606802 ∙ HGNC:11242 ∙ Uniprot:Q01892 ∙ 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 SPIB gene.

• Inborn genetic diseases (8 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPIB 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				2	1	3
missense			7	2	1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1		1
Total	0	0	7	5	2

Variants in SPIB

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

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

Position	Type	Phenotype	Significance	ClinVar
19-50419939-C-T			Benign (Apr 16, 2018)
19-50419955-G-A			Likely benign (Jun 11, 2018)
19-50419983-G-A			Likely benign (Jun 13, 2018)
19-50422483-G-A			Likely benign (Aug 01, 2018)
19-50422504-G-A		not specified	Uncertain significance (Sep 22, 2023)
19-50422867-C-T		not specified	Likely benign (Jan 03, 2024)
19-50422868-C-G		not specified	Uncertain significance (Jan 26, 2022)
19-50422871-A-G		not specified	Uncertain significance (Jun 18, 2021)
19-50422897-G-A		not specified	Likely benign (Dec 06, 2021)
19-50423007-T-T			Benign (Dec 31, 2019)
19-50423008-G-C			Benign (Oct 30, 2019)
19-50423036-A-T		not specified	Uncertain significance (Apr 28, 2023)
19-50423712-T-C			Likely benign (Aug 07, 2018)
19-50423731-C-T		not specified	Uncertain significance (Aug 17, 2022)
19-50423748-C-T			Benign (Jul 11, 2018)
19-50428047-A-C		not specified	Uncertain significance (Feb 14, 2023)
19-50428091-G-A		not specified	Uncertain significance (Jun 14, 2023)
19-50428175-C-A		not specified	Uncertain significance (Aug 02, 2022)
19-50428325-C-T		not specified	Uncertain significance (Apr 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPIB	protein_coding	protein_coding	ENST00000595883	6	12376

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.912	0.0876	112437	0	1	112438	0.00000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.26	110	154	0.714	0.00000937	1633
Missense in Polyphen		36	66.967	0.53758		725
Synonymous	0.675	67	74.4	0.901	0.00000517	534
Loss of Function	2.98	1	12.2	0.0818	5.22e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000722	0.0000722
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: Sequence specific transcriptional activator which binds to the PU-box, a purine-rich DNA sequence (5'-GAGGAA-3') that can act as a lymphoid-specific enhancer. Promotes development of plasmacytoid dendritic cells (pDCs), also known as type 2 DC precursors (pre-DC2) or natural interferon (IFN)-producing cells. These cells have the capacity to produce large amounts of interferon and block viral replication. May be required for B-cell receptor (BCR) signaling, which is necessary for normal B-cell development and antigenic stimulation. {ECO:0000269|PubMed:10196196, ECO:0000269|PubMed:12393575, ECO:0000269|PubMed:1406622, ECO:0000269|PubMed:15583020}.

Recessive Scores

• pRec: 0.186

Intolerance Scores

• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.539
• hipred: Y
• hipred_score: 0.519
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.814

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spib
• 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); hematopoietic system phenotype; immune system phenotype; digestive/alimentary phenotype; cellular phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;cell differentiation;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA polymerase II distal enhancer sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific