FOCAD

focadhesin, the group of Small nucleolar RNA protein coding host genes|Armadillo like helical domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 9:20658308-20995955

Previous symbols: [ "KIAA1797" ]

Links

ENSG00000188352 ∙ NCBI:54914 ∙ OMIM:614606 ∙ HGNC:23377 ∙ Uniprot:Q5VW36 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• liver disease, severe congenital (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Liver disease, severe congenital	AR	Gastrointestinal	The condition can involve severe, early-onset hepatic disease, and awareness may allow prompt managment of liver disease and related sequelae	Gastrointestinal	35864190

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FOCAD gene.

• not provided (185 variants)
• Inborn genetic diseases (83 variants)
• FOCAD-related condition (18 variants)
• not specified (3 variants)
• - (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FOCAD 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	16	9	27
missense			112	16	14	142
nonsense			1			1
start loss						0
frameshift			2			2
inframe indel			1			1
splice donor/acceptor (+/-2bp)			1			1
splice region			3	12	2	17
non coding				11	75	86
Total	0	0	119	43	98

Variants in FOCAD

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

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

Position	Type	Phenotype	Significance	ClinVar
9-20715278-G-T			Benign (Jul 26, 2019)
9-20715313-T-C			Benign (Jun 14, 2019)
9-20715373-A-T			Uncertain significance (Jan 07, 2024)
9-20715402-C-A		FOCAD-related disorder • Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
9-20715404-A-G			Uncertain significance (Dec 29, 2023)
9-20717795-C-G		Inborn genetic diseases	Uncertain significance (Feb 15, 2023)
9-20717858-C-A		Inborn genetic diseases	Uncertain significance (Oct 17, 2023)
9-20720318-GGT-G			Benign (Sep 05, 2019)
9-20720368-G-A			Likely benign (Jan 29, 2024)
9-20720370-T-G		FOCAD-related disorder	Likely benign (Jun 20, 2019)
9-20720389-T-C		FOCAD-related disorder	Likely benign (May 23, 2019)
9-20720423-A-G		Inborn genetic diseases	Uncertain significance (Feb 15, 2023)
9-20720441-C-T		Inborn genetic diseases	Uncertain significance (Nov 17, 2022)
9-20720467-G-A			Uncertain significance (Dec 18, 2023)
9-20720506-G-A			Uncertain significance (Dec 14, 2023)
9-20720523-T-TC			Uncertain significance (Jan 07, 2024)
9-20720600-A-C			Benign (Jun 14, 2019)
9-20740078-G-A			Benign (Jun 14, 2019)
9-20740265-T-C		Inborn genetic diseases	Uncertain significance (May 06, 2022)
9-20740267-C-T		FOCAD-related disorder	Likely benign (Mar 29, 2023)
9-20740269-C-G		Inborn genetic diseases	Uncertain significance (Mar 01, 2023)
9-20740273-C-A		FOCAD-related disorder	Uncertain significance (Dec 12, 2023)
9-20740318-A-G			Uncertain significance (Jan 03, 2024)
9-20740322-A-G		Inborn genetic diseases	Uncertain significance (Jan 26, 2024)
9-20740324-A-G			Likely benign (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FOCAD	protein_coding	protein_coding	ENST00000380249	43	337647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.21e-37	0.278	125577	0	171	125748	0.000680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.93	1182	931	1.27	0.0000463	11679
Missense in Polyphen		292	254.84	1.1458		3271
Synonymous	-2.61	400	339	1.18	0.0000174	3536
Loss of Function	2.59	72	99.9	0.720	0.00000499	1202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00146	0.00145
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000295	0.000272
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000746	0.000721
Middle Eastern	0.000295	0.000272
South Asian	0.00119	0.00118
Other	0.000654	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential tumor suppressor in gliomas. {ECO:0000250, ECO:0000269|PubMed:22427331}.

Recessive Scores

• pRec: 0.0800

Intolerance Scores

• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.26

Haploinsufficiency Scores

• pHI: 0.0701
• hipred: N
• hipred_score: 0.492
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Focad

Gene ontology

• Cellular component: focal adhesion;integral component of membrane
• Molecular function: protein binding