COTL1

coactosin like F-actin binding protein 1

Basic information

Region (hg38): 16:84565596-84618078

Links

ENSG00000103187

∙ NCBI:23406 ∙ OMIM:606748 ∙ HGNC:18304 ∙ Uniprot:Q14019 ∙ 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 COTL1 gene.

not_specified (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COTL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021149.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			22 clinvar			22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COTL1	protein_coding	protein_coding	ENST00000262428	4	52484

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0391	0.849	125410	0	4	125414	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.125	101	97.5	1.04	0.00000636	922
Missense in Polyphen		23	30.94	0.74338		300
Synonymous	-1.50	56	43.4	1.29	0.00000328	261
Loss of Function	1.28	3	6.55	0.458	2.77e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Binds to F-actin in a calcium-independent manner. Has no direct effect on actin depolymerization. Acts as a chaperone for ALOX5 (5LO), influencing both its stability and activity in leukotrienes synthesis. {ECO:0000269|PubMed:11583571, ECO:0000269|PubMed:19807693}.;
Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

pRec: 0.145

Intolerance Scores

loftool: 0.281
rvis_EVS: -0.23
rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

pHI: 0.216
hipred: Y
hipred_score: 0.582
ghis: 0.632

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cotl1
Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); vision/eye phenotype; pigmentation phenotype;

Gene ontology

Biological process: biological_process;neutrophil degranulation;defense response to fungus
Cellular component: extracellular region;nucleus;cytoskeleton;secretory granule lumen;extracellular exosome;ficolin-1-rich granule lumen
Molecular function: actin binding;protein binding;enzyme binding