FIGNL1

fidgetin like 1, the group of AAA ATPases

Basic information

Region (hg38): 7:50444128-50450390

Links

ENSG00000132436 ∙ NCBI:63979 ∙ OMIM:615383 ∙ HGNC:13286 ∙ Uniprot:Q6PIW4 ∙ 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 FIGNL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FIGNL1 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			54	4		58
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	4	1

Variants in FIGNL1

This is a list of pathogenic ClinVar variants found in the FIGNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-50445316-T-G		not specified	Uncertain significance (Jan 19, 2024)
7-50445366-T-C		not specified	Uncertain significance (Jun 07, 2023)
7-50445390-G-A		not specified	Uncertain significance (Nov 30, 2021)
7-50445462-G-A		not specified	Uncertain significance (May 26, 2022)
7-50445463-T-C		not specified	Uncertain significance (Apr 09, 2024)
7-50445466-T-C		not specified	Uncertain significance (Feb 05, 2024)
7-50445483-G-A		not specified	Uncertain significance (Oct 13, 2023)
7-50445499-C-T		not specified	Uncertain significance (Oct 19, 2024)
7-50445504-T-C		not specified	Uncertain significance (May 27, 2022)
7-50445523-T-A		not specified	Uncertain significance (Jul 23, 2024)
7-50445660-C-T		not specified	Uncertain significance (Oct 03, 2022)
7-50445675-C-T		not specified	Uncertain significance (Nov 18, 2022)
7-50445676-G-A		not specified	Uncertain significance (Mar 29, 2023)
7-50445678-T-C		not specified	Uncertain significance (Mar 02, 2023)
7-50445754-C-T		not specified	Uncertain significance (Oct 05, 2023)
7-50445764-TTGAGA-T		not specified	Uncertain significance (Mar 25, 2015)
7-50445777-G-A		not specified	Uncertain significance (Oct 17, 2023)
7-50445799-T-C		not specified	Uncertain significance (Nov 07, 2023)
7-50445810-T-C		not specified	Uncertain significance (Oct 19, 2024)
7-50445823-C-T		not specified	Uncertain significance (Sep 01, 2024)
7-50445840-C-T		not specified	Uncertain significance (Feb 25, 2025)
7-50445859-C-T		not specified	Uncertain significance (Nov 17, 2022)
7-50445871-T-G		not specified	Uncertain significance (Jan 04, 2024)
7-50445939-A-G		not specified	Uncertain significance (Oct 12, 2024)
7-50445972-A-G		not specified	Uncertain significance (Feb 10, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FIGNL1	protein_coding	protein_coding	ENST00000419119	1	6258

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000120	0.991	125592	0	155	125747	0.000617

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.522	389	361	1.08	0.0000185	4420
Missense in Polyphen		99	106.48	0.92977		1242
Synonymous	-0.376	129	124	1.04	0.00000587	1345
Loss of Function	2.30	10	21.5	0.464	0.00000122	261

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000601	0.000601
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000326	0.000326
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000916	0.000915
Middle Eastern	0.000326	0.000326
South Asian	0.000654	0.000653
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in DNA double-strand break (DBS) repair via homologous recombination (HR). Recruited at DSB sites independently of BRCA2, RAD51 and RAD51 paralogs in a H2AX- dependent manner. May regulate osteoblast proliferation and differentiation (PubMed:23754376). May play a role in the control of male meiosis dynamic (By similarity). {ECO:0000250|UniProtKB:Q8BPY9, ECO:0000269|PubMed:23754376}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.0886
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.71

Haploinsufficiency Scores

• pHI: 0.473
• hipred: N
• hipred_score: 0.251
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.125

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fignl1

Gene ontology

• Biological process: osteoblast differentiation;male meiotic nuclear division;regulation of double-strand break repair via homologous recombination;cytoplasmic microtubule organization;osteoblast proliferation;negative regulation of apoptotic process;ATP metabolic process;microtubule severing;regulation of cell cycle;cellular response to ionizing radiation;negative regulation of intrinsic apoptotic signaling pathway
• Cellular component: nuclear chromosome;nucleus;cytoplasm;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: magnesium ion binding;protein binding;ATP binding;microtubule-severing ATPase activity;hydrolase activity;ATPase activity