CTNNAL1

catenin alpha like 1

Basic information

Region (hg38): 9:108942569-109013522

Links

ENSG00000119326 ∙ NCBI:8727 ∙ OMIM:604785 ∙ HGNC:2512 ∙ Uniprot:Q9UBT7 ∙ 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 CTNNAL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTNNAL1 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						0
missense			34	1	1	36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	34	1	1

Variants in CTNNAL1

This is a list of pathogenic ClinVar variants found in the CTNNAL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-108943762-G-C		not specified	Uncertain significance (May 11, 2022)
9-108943764-G-A		not specified	Uncertain significance (Jun 07, 2023)
9-108943808-G-C		not specified	Uncertain significance (Jan 23, 2024)
9-108943978-T-C		not specified	Uncertain significance (Oct 09, 2024)
9-108943981-A-C		not specified	Uncertain significance (Sep 16, 2021)
9-108943990-G-A		not specified	Uncertain significance (Jan 30, 2024)
9-108943994-G-A		not specified	Uncertain significance (Jun 24, 2022)
9-108952266-A-T		not specified	Uncertain significance (Mar 19, 2024)
9-108952277-C-G		not specified	Uncertain significance (Nov 15, 2021)
9-108952296-A-G		not specified	Uncertain significance (Nov 07, 2024)
9-108952350-A-G		not specified	Uncertain significance (Apr 13, 2022)
9-108952478-A-T		not specified	Uncertain significance (Jan 19, 2022)
9-108965380-C-T		not specified	Uncertain significance (Dec 03, 2024)
9-108970475-T-C		not specified	Uncertain significance (Aug 13, 2021)
9-108970484-A-G		not specified	Uncertain significance (Dec 16, 2022)
9-108970487-C-T		not specified	Uncertain significance (Apr 07, 2022)
9-108972724-A-C		not specified	Uncertain significance (Jan 18, 2022)
9-108972751-G-C			Benign (Jul 31, 2018)
9-108972757-T-G		not specified	Uncertain significance (Apr 04, 2023)
9-108972758-T-C		not specified	Uncertain significance (Aug 28, 2024)
9-108972840-ATG-A			Benign (Jul 23, 2018)
9-108977024-C-T		not specified	Uncertain significance (Mar 31, 2023)
9-108977048-G-C		not specified	Uncertain significance (Oct 09, 2024)
9-108979330-G-A		not specified	Uncertain significance (Apr 07, 2023)
9-108979399-C-A		not specified	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTNNAL1	protein_coding	protein_coding	ENST00000325551	19	70959

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.74e-10	0.990	125683	0	64	125747	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.688	317	353	0.897	0.0000172	4777
Missense in Polyphen		113	137.92	0.81933		1920
Synonymous	0.757	116	127	0.914	0.00000655	1371
Loss of Function	2.46	22	38.5	0.572	0.00000194	515

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000640	0.000635
Ashkenazi Jewish	0.00	0.00
East Asian	0.000385	0.000381
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000343	0.000325
Middle Eastern	0.000385	0.000381
South Asian	0.000135	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May modulate the Rho pathway signaling by providing a scaffold for the Lbc Rho guanine nucleotide exchange factor (ARHGEF1).
• Pathway: Regulation of toll-like receptor signaling pathway;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.951
• rvis_EVS: -0.04
• rvis_percentile_EVS: 50.45

Haploinsufficiency Scores

• pHI: 0.227
• hipred: Y
• hipred_score: 0.540
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.576

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctnnal1
• Phenotype: normal phenotype

Gene ontology

• Biological process: cell adhesion;Rho protein signal transduction
• Cellular component: cytosol;cytoskeleton;plasma membrane
• Molecular function: protein binding;cadherin binding;actin filament binding