FANK1

fibronectin type III and ankyrin repeat domains 1, the group of Ankyrin repeat domain containing|Fibronectin type III domain containing

Basic information

Region (hg38): 10:125896563-126009592

Links

ENSG00000203780 ∙ NCBI:92565 ∙ OMIM:611640 ∙ HGNC:23527 ∙ Uniprot:Q8TC84 ∙ 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 FANK1 gene.

• Inborn genetic diseases (11 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FANK1 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	2
missense			11		1	12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	3

Variants in FANK1

This is a list of pathogenic ClinVar variants found in the FANK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-125980184-C-T		not specified	Uncertain significance (Feb 21, 2024)
10-125980253-A-G		not specified	Uncertain significance (Dec 09, 2023)
10-125980257-G-A		not specified	Uncertain significance (Feb 11, 2022)
10-125980290-C-T		not specified	Uncertain significance (Apr 11, 2023)
10-125980293-T-C		not specified	Uncertain significance (Nov 13, 2023)
10-125980315-G-A		not specified	Uncertain significance (May 23, 2023)
10-125980324-T-C			Benign (Jan 08, 2018)
10-125988628-C-T		not specified	Uncertain significance (Jan 30, 2024)
10-125988651-C-T		not specified	Uncertain significance (Mar 04, 2024)
10-125995420-A-G		not specified	Uncertain significance (Jul 19, 2022)
10-125995447-G-A		not specified	Uncertain significance (Dec 11, 2023)
10-125996566-G-A		not specified	Uncertain significance (Jan 26, 2022)
10-125996569-C-G		not specified	Uncertain significance (Feb 15, 2023)
10-126004895-C-T		not specified	Uncertain significance (Nov 30, 2022)
10-126004905-G-A			Benign (Jun 15, 2018)
10-126004934-G-A		not specified	Uncertain significance (Jun 30, 2023)
10-126008437-A-T		not specified	Uncertain significance (Nov 10, 2022)
10-126008459-C-T		not specified	Uncertain significance (Jan 31, 2022)
10-126008488-C-T		not specified	Uncertain significance (Feb 28, 2024)
10-126009074-T-G		not specified	Uncertain significance (Mar 28, 2022)
10-126009428-G-T			Benign (Jun 05, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FANK1	protein_coding	protein_coding	ENST00000368693	11	113054

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.68e-9	0.391	125338	1	409	125748	0.00163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.555	173	195	0.888	0.0000106	2237
Missense in Polyphen		76	85.691	0.8869		972
Synonymous	0.750	62	70.0	0.886	0.00000390	657
Loss of Function	0.937	16	20.6	0.777	0.00000114	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00142	0.00142
Ashkenazi Jewish	0.00189	0.00189
East Asian	0.000381	0.000381
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.00249	0.00249
Middle Eastern	0.000381	0.000381
South Asian	0.00156	0.00150
Other	0.00180	0.00179

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Through the activation of JUN and AP-1-mediated transcription, may regulate apoptosis. {ECO:0000269|PubMed:20978819, ECO:0000269|PubMed:27060496}.

Recessive Scores

• pRec: 0.0941

Intolerance Scores

• loftool: 0.893
• rvis_EVS: 1.64
• rvis_percentile_EVS: 96.15

Haploinsufficiency Scores

• pHI: 0.249
• hipred: N
• hipred_score: 0.369

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fank1

Gene ontology

• Biological process: positive regulation of apoptotic process;negative regulation of apoptotic process;positive regulation of transcription, DNA-templated;positive regulation of DNA-binding transcription factor activity
• Cellular component: chromatin;nucleus;nucleoplasm;cytoplasm;cytosol;cilium;ciliary basal body
• Molecular function: protein binding