FBLIM1

filamin binding LIM protein 1, the group of LIM domain containing

Basic information

Region (hg38): 1:15756607-15786594

Links

ENSG00000162458 ∙ NCBI:54751 ∙ OMIM:607747 ∙ HGNC:24686 ∙ Uniprot:Q8WUP2 ∙ 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 FBLIM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBLIM1 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	3
missense			24		3	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	6

Variants in FBLIM1

This is a list of pathogenic ClinVar variants found in the FBLIM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-15765006-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-15765096-G-A		not specified	Uncertain significance (Sep 08, 2022)
1-15765098-C-T			Benign (Aug 08, 2017)
1-15765105-G-A		not specified	Uncertain significance (Apr 17, 2024)
1-15765205-G-A			Benign (May 31, 2018)
1-15765216-T-C		not specified	Uncertain significance (Feb 12, 2024)
1-15767414-G-A		not specified	Uncertain significance (Feb 22, 2023)
1-15767441-C-T		not specified	Uncertain significance (May 23, 2023)
1-15767465-C-T		not specified	Uncertain significance (Jan 03, 2022)
1-15767505-C-T		not specified	Uncertain significance (Aug 01, 2022)
1-15767510-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-15768557-C-T			Benign (Jul 31, 2018)
1-15768558-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-15768559-G-A		not specified	Uncertain significance (Feb 26, 2024)
1-15768609-G-A			Benign (Jan 19, 2018)
1-15770465-A-G		not specified	Uncertain significance (Oct 25, 2022)
1-15770502-G-A		not specified	Uncertain significance (Feb 01, 2023)
1-15770511-G-A		not specified	Uncertain significance (Feb 17, 2024)
1-15770525-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
1-15770532-G-A		not specified	Uncertain significance (Oct 18, 2021)
1-15770553-G-A		not specified	Uncertain significance (Nov 09, 2021)
1-15774636-G-A		not specified	Uncertain significance (May 20, 2024)
1-15774657-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-15774723-G-A		not specified	Uncertain significance (May 15, 2024)
1-15774726-C-T		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBLIM1	protein_coding	protein_coding	ENST00000441801	5	29988

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000539	0.699	125677	0	64	125741	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.526	198	220	0.900	0.0000133	2349
Missense in Polyphen		57	76.706	0.74309		828
Synonymous	0.266	88	91.2	0.965	0.00000585	792
Loss of Function	0.958	8	11.5	0.695	6.60e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00110	0.00110
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000140	0.000139
European (Non-Finnish)	0.0000806	0.0000791
Middle Eastern	0.000163	0.000163
South Asian	0.000588	0.000588
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serves as an anchoring site for cell-ECM adhesion proteins and filamin-containing actin filaments. Is implicated in cell shape modulation (spreading) and motility. May participate in the regulation of filamin-mediated cross-linking and stabilization of actin filaments. May also regulate the assembly of filamin- containing signaling complexes that control actin assembly. Promotes dissociation of FLNA from ITGB3 and ITGB7. Promotes activation of integrins and regulates integrin-mediated cell-cell adhesion. {ECO:0000269|PubMed:12496242, ECO:0000269|PubMed:12679033, ECO:0000269|PubMed:18829455, ECO:0000269|PubMed:19074766}.
• Pathway: Cell-extracellular matrix interactions;Cell junction organization;Cell-Cell communication (Consensus)

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.229
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.24

Haploinsufficiency Scores

• pHI: 0.304
• hipred: Y
• hipred_score: 0.511
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.434

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fblim1
• Phenotype: immune system phenotype; skeleton phenotype; normal phenotype; hematopoietic system phenotype; cellular phenotype

Gene ontology

• Biological process: regulation of cell shape;regulation of integrin activation;cell junction assembly;cell-cell adhesion
• Cellular component: fibrillar center;stress fiber;cytosol;focal adhesion;cell junction
• Molecular function: protein binding;filamin binding;metal ion binding