BASP1

brain abundant membrane attached signal protein 1

Basic information

Region (hg38): 5:17065597-17276843

Links

ENSG00000176788 ∙ NCBI:10409 ∙ OMIM:605940 ∙ HGNC:957 ∙ Uniprot:P80723 ∙ 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 BASP1 gene.

• Inborn genetic diseases (9 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BASP1 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					1	1
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	1

Variants in BASP1

This is a list of pathogenic ClinVar variants found in the BASP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-17275255-T-C			Benign (May 24, 2018)
5-17275337-G-C		not specified	Uncertain significance (Nov 09, 2023)
5-17275388-C-T		not specified	Uncertain significance (Nov 21, 2023)
5-17275455-A-C		not specified	Uncertain significance (Jun 24, 2022)
5-17275456-G-C		not specified	Uncertain significance (Dec 27, 2022)
5-17275493-G-A		not specified	Uncertain significance (Apr 19, 2023)
5-17275514-C-T		not specified	Uncertain significance (Oct 16, 2023)
5-17275584-C-G		not specified	Uncertain significance (Feb 05, 2024)
5-17275595-G-A		not specified	Uncertain significance (Sep 17, 2021)
5-17275613-G-A		not specified	Uncertain significance (Feb 28, 2023)
5-17275616-G-A		not specified	Uncertain significance (Jun 28, 2023)
5-17275619-C-T		not specified	Uncertain significance (Jan 24, 2024)
5-17275637-C-T		not specified	Uncertain significance (Jul 25, 2023)
5-17275662-A-G		not specified	Uncertain significance (Nov 29, 2023)
5-17275680-C-T		not specified	Uncertain significance (Feb 23, 2023)
5-17275691-G-A		not specified	Uncertain significance (Sep 16, 2021)
5-17275757-C-T		not specified	Uncertain significance (Nov 13, 2023)
5-17275821-C-T		not specified	Uncertain significance (Jan 02, 2024)
5-17275883-G-C		not specified	Uncertain significance (Feb 06, 2024)
5-17275889-G-T		Inborn genetic diseases	Uncertain significance (Jun 22, 2015)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BASP1	protein_coding	protein_coding	ENST00000322611	1	211237

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.692	0.292	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.351	130	119	1.09	0.00000802	1421
Missense in Polyphen		20	26.225	0.76264		268
Synonymous	0.881	56	65.0	0.861	0.00000608	456
Loss of Function	1.82	0	3.86	0.00	1.59e-7	81

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
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

Recessive Scores

• pRec: 0.138

Haploinsufficiency Scores

• pHI: 0.202
• hipred: N
• hipred_score: 0.326
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.453

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Basp1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype

Gene ontology

• Biological process: thorax and anterior abdomen determination;gonad development;substantia nigra development;negative regulation of transcription, DNA-templated;mesenchymal to epithelial transition;positive regulation of heart growth;diaphragm development;metanephric mesenchyme development;glomerular visceral epithelial cell differentiation;positive regulation of metanephric ureteric bud development
• Cellular component: nucleus;cytoplasm;cytoskeleton;plasma membrane;COP9 signalosome;nuclear speck;cell junction;growth cone;vesicle;extracellular exosome
• Molecular function: transcription corepressor activity;protein binding;protein domain specific binding;transcription regulatory region DNA binding