SPTBN5

spectrin beta, non-erythrocytic 5, the group of MicroRNA protein coding host genes|Spectrins

Basic information

Region (hg38): 15:41848145-41894053

Links

ENSG00000137877 ∙ NCBI:51332 ∙ OMIM:605916 ∙ HGNC:15680 ∙ Uniprot:Q9NRC6 ∙ 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 SPTBN5 gene.

• Inborn genetic diseases (236 variants)
• not provided (74 variants)
• SPTBN5-related condition (4 variants)
• See cases (2 variants)
• Intellectual disability, moderate;Autistic behavior;Autism;Delayed speech and language development;Premature birth (1 variants)
• Intellectual disability, moderate;Autism;Premature birth;Delayed speech and language development;Autistic behavior (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPTBN5 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	13	11	26
missense			202	46	22	270
nonsense			2		1	3
start loss						0
frameshift			4			4
inframe indel						0
splice donor/acceptor (+/-2bp)			2		1	3
splice region					2	2
non coding					4	4
Total	0	0	212	59	39

Variants in SPTBN5

This is a list of pathogenic ClinVar variants found in the SPTBN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-41849891-C-A		not specified	Uncertain significance (Nov 03, 2023)
15-41849902-G-A			Benign (Nov 01, 2023)
15-41849904-G-A		SPTBN5-related disorder	Likely benign (May 10, 2022)
15-41849956-T-A		not specified	Uncertain significance (Nov 29, 2023)
15-41850869-G-C		not specified	Uncertain significance (Jan 22, 2024)
15-41850879-C-T			Uncertain significance (Feb 27, 2023)
15-41850903-C-T		SPTBN5-related disorder	Likely benign (Jan 06, 2020)
15-41850904-G-A		not specified	Uncertain significance (Aug 04, 2023)
15-41850920-T-C		SPTBN5-related disorder	Benign (Dec 06, 2019)
15-41850923-C-G		not specified	Uncertain significance (Nov 09, 2021)
15-41850928-C-T		not specified	Uncertain significance (Feb 07, 2023)
15-41850929-C-G		not specified	Uncertain significance (Feb 05, 2024)
15-41850931-C-G		not specified	Uncertain significance (Apr 25, 2023)
15-41850933-G-T			Likely benign (Nov 01, 2022)
15-41851065-G-A		not specified	Uncertain significance (Sep 22, 2023)
15-41851089-C-A		not specified	Uncertain significance (Nov 10, 2022)
15-41851090-G-A		not specified	Likely benign (Dec 03, 2021)
15-41851092-C-T		not specified	Likely benign (Aug 10, 2023)
15-41851095-C-T		SPTBN5-related disorder	Likely benign (Feb 21, 2023)
15-41851111-G-A		not specified	Uncertain significance (Aug 12, 2021)
15-41851137-A-G		not specified	Likely benign (Oct 03, 2022)
15-41851139-G-A		SPTBN5-related disorder	Likely benign (Apr 10, 2019)
15-41851307-G-A			Likely benign (Jul 01, 2022)
15-41851326-C-T		not specified	Uncertain significance (Nov 17, 2023)
15-41851335-T-G			Benign (Apr 24, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPTBN5	protein_coding	protein_coding	ENST00000320955	67	45931

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.22e-118	1.84e-16	121706	35	2959	124700	0.0121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.24	2146	1.99e+3	1.08	0.000129	23174
Missense in Polyphen		519	510.94	1.0158		7261
Synonymous	-1.01	903	865	1.04	0.0000532	7416
Loss of Function	0.772	186	198	0.941	0.0000104	2021

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0133	0.0127
Ashkenazi Jewish	0.00612	0.00608
East Asian	0.0365	0.0361
Finnish	0.0123	0.0113
European (Non-Finnish)	0.00450	0.00436
Middle Eastern	0.0365	0.0361
South Asian	0.0403	0.0397
Other	0.0119	0.0114

dbNSFP

Source: dbNSFP

• Pathway: Developmental Biology;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Interaction between L1 and Ankyrins;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;NCAM signaling for neurite out-growth;L1CAM interactions;COPI-mediated anterograde transport;Axon guidance;ER to Golgi Anterograde Transport (Consensus)

Recessive Scores

• pRec: 0.121

Haploinsufficiency Scores

• pHI: 0.169
• hipred: N
• hipred_score: 0.146
• ghis: 0.481

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Sptbn5

Gene ontology

• Biological process: MAPK cascade;endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi organization;lysosomal transport;axon guidance;actin cytoskeleton organization;protein homooligomerization;actin filament capping
• Cellular component: cytoplasm;microtubule organizing center;cytosol;spectrin;membrane;filamentous actin;photoreceptor connecting cilium;photoreceptor disc membrane
• Molecular function: actin binding;Ras guanyl-nucleotide exchange factor activity;kinesin binding;spectrin binding;myosin tail binding;dynactin binding;protein self-association;dynein intermediate chain binding