FLACC1

flagellum associated containing coiled-coil domains 1

Basic information

Region (hg38): 2:201288270-201357398

Previous symbols: [ "ALS2CR12" ]

Links

ENSG00000155749 ∙ NCBI:130540 ∙ OMIM:619796 ∙ HGNC:14439 ∙ Uniprot:Q96Q35 ∙ 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 FLACC1 gene.

• Inborn genetic diseases (11 variants)
• not specified (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 FLACC1 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	2
missense			9	2		11
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	3	1

Variants in FLACC1

This is a list of pathogenic ClinVar variants found in the FLACC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-201288668-C-T		not specified	Uncertain significance (Jun 29, 2023)
2-201288672-T-C		not specified	Uncertain significance (Feb 15, 2023)
2-201288680-C-T		not specified	Uncertain significance (Sep 20, 2023)
2-201288683-T-G		not specified	Uncertain significance (Jul 20, 2021)
2-201288714-C-G		not specified	Uncertain significance (Jul 13, 2021)
2-201288740-C-T		not specified	Likely benign (Oct 17, 2023)
2-201289477-C-T		not specified	Benign (Mar 28, 2016)
2-201289509-C-T		not specified	Uncertain significance (Sep 29, 2022)
2-201289518-C-T		not specified	Uncertain significance (Nov 22, 2023)
2-201289524-A-G		not specified	Likely benign (Mar 06, 2023)
2-201289560-T-C		not specified	Uncertain significance (Dec 16, 2023)
2-201289731-T-C		not specified	Uncertain significance (Mar 20, 2023)
2-201289745-T-C		not specified	Uncertain significance (Jul 25, 2023)
2-201289767-G-A		not specified	Uncertain significance (Nov 07, 2022)
2-201289815-C-G		not specified	Uncertain significance (Oct 12, 2022)
2-201307523-T-A		not specified	Uncertain significance (Nov 09, 2021)
2-201307527-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-201307533-T-C		not specified	Uncertain significance (Sep 26, 2022)
2-201330477-G-A		not specified	Likely benign (Mar 06, 2023)
2-201330770-C-G		not specified	Uncertain significance (Jan 06, 2023)
2-201330806-T-G		not specified	Uncertain significance (Feb 05, 2024)
2-201346565-G-C		not specified	Uncertain significance (Sep 16, 2021)
2-201346574-T-A		not specified	Uncertain significance (Jan 27, 2022)
2-201346614-G-C		not specified	Uncertain significance (Mar 24, 2023)
2-201346632-C-G		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FLACC1	protein_coding	protein_coding	ENST00000405148	14	69128

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-22	0.000325	125526	1	221	125748	0.000883

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.199	241	232	1.04	0.0000118	2976
Missense in Polyphen		71	63.679	1.115		856
Synonymous	-0.0574	80	79.3	1.01	0.00000399	734
Loss of Function	-0.445	32	29.4	1.09	0.00000133	363

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00416	0.00410
Ashkenazi Jewish	0.00486	0.00487
East Asian	0.00136	0.00136
Finnish	0.00	0.00
European (Non-Finnish)	0.000431	0.000431
Middle Eastern	0.00136	0.00136
South Asian	0.000622	0.000621
Other	0.000814	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0585

Intolerance Scores

• loftool: 0.992
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.08

Haploinsufficiency Scores

• pHI: 0.0186
• hipred: N
• hipred_score: 0.123
• ghis: 0.439

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0176

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Als2cr12

Gene ontology

• Cellular component: cellular_component;cytoplasm;motile cilium
• Molecular function: molecular_function;protein binding