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): 9:20658309-20995955

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 (533 variants)
• Inborn_genetic_diseases (291 variants)
• FOCAD-related_disorder (141 variants)
• Liver_disease,_severe_congenital (16 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. These statistics are base on transcript: NM_001375567.1. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			42	75	11	128
missense	1		441	41	12	495
nonsense	2	1	9			12
start loss						0
frameshift	2	2	7			11
splice donor/acceptor (+/-2bp)	2	3	7			12
Total	7	6	506	116	23

Highest pathogenic variant AF is 0.0000061961937

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