ARVCF

ARVCF delta catenin family member, the group of Armadillo like helical domain containing|p120 catenin family|Armadillo repeat containing

Basic information

Region (hg38): 22:19969895-20016823

Links

ENSG00000099889 ∙ NCBI:421 ∙ OMIM:602269 ∙ HGNC:728 ∙ Uniprot:O00192 ∙ 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 ARVCF gene.

• not provided (74 variants)
• Inborn genetic diseases (60 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARVCF 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				5	8	13
missense			62	5	9	76
nonsense						0
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1	1	2
non coding				1	39	40
Total	0	0	65	11	56

Variants in ARVCF

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

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

Position	Type	Phenotype	Significance	ClinVar
22-19969905-T-C		Tramadol response	drug response (Apr 28, 2018)
22-19969950-A-C		Tramadol response	drug response (Apr 28, 2018)
22-19969993-T-C		Tramadol response	drug response (Apr 28, 2018)
22-19970009-G-A		Tramadol response	drug response (Apr 28, 2018)
22-19970014-G-A		Tramadol response	drug response (Apr 28, 2018)
22-19970020-CA-C		Tramadol response	drug response (Apr 28, 2018)
22-19970064-C-A		Tramadol response	drug response (Apr 28, 2018)
22-19970080-G-A		Tramadol response	drug response (Apr 28, 2018)
22-19970084-C-A		Tramadol response	drug response (Apr 28, 2018)
22-19970097-CA-C		Tramadol response	drug response (Apr 28, 2018)
22-19970103-CG-C		Tramadol response	drug response (Apr 28, 2018)
22-19971145-CGG-C			Benign (May 11, 2021)
22-19971146-G-A			Benign (May 10, 2021)
22-19971245-C-T		not specified	Uncertain significance (Oct 03, 2022)
22-19971269-C-T		not specified	Uncertain significance (Jan 20, 2023)
22-19971271-G-A		not specified	Uncertain significance (Dec 14, 2023)
22-19971306-G-A			Benign (May 04, 2021)
22-19971314-G-A		not specified	Uncertain significance (May 31, 2023)
22-19971320-T-C		not specified	Uncertain significance (Aug 17, 2022)
22-19971488-G-A			Benign (May 10, 2021)
22-19971510-G-A			Benign (May 10, 2021)
22-19971704-G-A			Benign (May 10, 2021)
22-19971843-G-A			Benign (May 10, 2021)
22-19971903-C-T		not specified	Uncertain significance (Dec 20, 2023)
22-19971932-C-T		not specified	Uncertain significance (Feb 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARVCF	protein_coding	protein_coding	ENST00000263207	17	46913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.04e-11	0.988	125555	0	187	125742	0.000744

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.270	674	655	1.03	0.0000478	6009
Missense in Polyphen		276	289.56	0.95316		2709
Synonymous	0.660	279	293	0.951	0.0000215	2140
Loss of Function	2.44	23	39.6	0.581	0.00000199	429

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000828	0.000823
Ashkenazi Jewish	0.000643	0.000596
East Asian	0.000287	0.000272
Finnish	0.00416	0.00417
European (Non-Finnish)	0.000412	0.000404
Middle Eastern	0.000287	0.000272
South Asian	0.000429	0.000359
Other	0.000497	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in protein-protein interactions at adherens junctions.

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.705
• rvis_EVS: -0.05
• rvis_percentile_EVS: 48.95

Haploinsufficiency Scores

• pHI: 0.263
• hipred: Y
• hipred_score: 0.714
• ghis: 0.599

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: 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: Arvcf
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype

Gene ontology

• Biological process: cell-cell junction assembly;cell adhesion;multicellular organism development;calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules;cell-cell adhesion
• Cellular component: nucleus;cytoplasm;plasma membrane;cell-cell junction;cell-cell adherens junction
• Molecular function: protein binding;cadherin binding