BFSP2

beaded filament structural protein 2, the group of Beaded filament structural proteins

Basic information

Region (hg38): 3:133400056-133475222

Links

ENSG00000170819 ∙ NCBI:8419 ∙ OMIM:603212 ∙ HGNC:1041 ∙ Uniprot:Q13515 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cataract 12 multiple types (Definitive), mode of inheritance: AD
• pulverulent cataract (Supportive), mode of inheritance: AD
• early-onset sutural cataract (Supportive), mode of inheritance: AD
• early-onset lamellar cataract (Supportive), mode of inheritance: AD
• cataract 12 multiple types (Definitive), mode of inheritance: AR
• cataract 12 multiple types (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 12, multiple types	AD/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	Ophthalmologic	10729115; 10739768; 10634598; 15570218; 17982427; 18958306; 21836522

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BFSP2 gene.

• Cataract 12 multiple types (2 variants)
• 7 conditions (1 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BFSP2 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			3	6	7	16
missense			42	5	3	50
nonsense	1		1			2
start loss						0
frameshift	1		2			3
inframe indel	1		2			3
splice donor/acceptor (+/-2bp)						0
splice region			2	2		4
non coding			4	14	19	37
Total	3	0	54	25	29

Variants in BFSP2

This is a list of pathogenic ClinVar variants found in the BFSP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-133400080-G-A		Cataract 12 multiple types	Likely benign (Jan 13, 2018)
3-133400088-G-A		Cataract 12 multiple types	Uncertain significance (Jan 13, 2018)
3-133400096-C-T		Cataract 12 multiple types	Uncertain significance (Mar 26, 2024)
3-133400107-G-A		Cataract 12 multiple types • BFSP2-related disorder	Likely benign (Oct 06, 2023)
3-133400110-C-G		Cataract 12 multiple types	Uncertain significance (May 03, 2021)
3-133400134-C-T		Cataract 12 multiple types	Likely benign (Nov 30, 2021)
3-133400158-G-A		Cataract 12 multiple types	Benign (Jan 17, 2024)
3-133400183-T-C		Cataract 12 multiple types • not specified	Conflicting classifications of pathogenicity (Feb 28, 2023)
3-133400213-A-G		not specified	Uncertain significance (Aug 10, 2023)
3-133400238-G-A		not specified	Uncertain significance (Jul 11, 2023)
3-133400245-C-T		Cataract 12 multiple types	Benign (Jan 15, 2024)
3-133400245-CG-C		Cataract 12 multiple types	Pathogenic (Sep 06, 2022)
3-133400246-G-A		not specified	Likely benign (Oct 03, 2022)
3-133400268-C-A		Cataract 12 multiple types	Uncertain significance (May 11, 2023)
3-133400273-G-T		Cataract 12 multiple types	Uncertain significance (Jul 26, 2022)
3-133400279-A-G		not specified	Uncertain significance (Mar 01, 2023)
3-133400298-G-A		Cataract 12 multiple types	Uncertain significance (Oct 31, 2022)
3-133400306-C-T		not specified	Uncertain significance (Jan 16, 2024)
3-133400310-G-A		not specified	Uncertain significance (Mar 29, 2023)
3-133400315-C-A		not specified	Uncertain significance (Sep 17, 2021)
3-133400318-G-A		not specified	Uncertain significance (Oct 03, 2022)
3-133400329-T-C		Cataract 12 multiple types	Benign (Nov 27, 2023)
3-133400332-C-CT		Cataract 12 multiple types	Uncertain significance (Apr 28, 2017)
3-133400337-T-A		not specified	Uncertain significance (Jul 05, 2023)
3-133400345-C-A		not specified	Uncertain significance (Oct 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BFSP2	protein_coding	protein_coding	ENST00000302334	7	75228

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.22e-8	0.772	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.292	239	252	0.948	0.0000161	2683
Missense in Polyphen		64	63.914	1.0013		770
Synonymous	0.917	88	99.6	0.883	0.00000613	855
Loss of Function	1.42	15	22.3	0.674	0.00000138	218

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000272	0.000272
Finnish	0.000305	0.000277
European (Non-Finnish)	0.000195	0.000185
Middle Eastern	0.000272	0.000272
South Asian	0.000261	0.000261
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in stabilization of lens fiber cell cytoskeleton. {ECO:0000250|UniProtKB:Q6NVD9}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.218
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.335
• hipred: N
• hipred_score: 0.237
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0918

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bfsp2
• Phenotype: vision/eye phenotype; cellular phenotype

Gene ontology

• Biological process: visual perception;intermediate filament cytoskeleton organization;cell maturation;response to stimulus;lens fiber cell development
• Cellular component: intermediate filament;plasma membrane;cell cortex
• Molecular function: structural constituent of cytoskeleton;structural constituent of eye lens;protein binding