FOCAD

protein-coding

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

Gene summary

Predicted to be involved in regulation of post-transcriptional gene silencing. Located in cytosol and focal adhesion. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KIAA1797

MANE transcript

NM_001375567.1

Inheritance

ClinVar variants

P:15U:642B:178

Top phenotype

Liver disease, severe congenital

gnomAD constraint

pLI —, LoF o/e 0.72

Max pathogenic AF

—

Genomic locus

chr9:20,658,309-20,995,955

External References & Databases

Ensembl (ENSG00000188352)

Transcript & Mutation Effects

hg38 • Region Span ~337.6 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

liver disease, severe congenitalSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0859273

Submitter: PanelApp Australia

liver disease, severe congenitalMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0859273

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Liver disease, severe congenitalAR

Manifestation: Gastrointestinal

Intervention: Gastrointestinal

Rationale: The condition can involve severe, early-onset hepatic disease, and awareness may allow prompt managment of liver disease and related sequelae

Refs: 35864190

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FOCAD variants in ClinVar

5 Conditions Cataloged

not providedTotal: 730

Inborn genetic diseasesTotal: 333

FOCAD-related disorderTotal: 157

Liver disease, severe congenitalTotal: 21

not specifiedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001375567.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			37 clinvar	116 clinvar	9 clinvar	162
missense	1 clinvar		567 clinvar	41 clinvar	12 clinvar	621
nonsense	2 clinvar	2 clinvar	14 clinvar			18
start loss						0
frameshift	2 clinvar	1 clinvar	8 clinvar			11
splice donor/acceptor (+/-2bp)	2 clinvar	5 clinvar	16 clinvar			23
Total	7	8	642	157	21	835

Highest pathogenic variant AF is 0.00010036826

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001375567.1	RefSeq	NP_001362496.1	43	MANE Select
ENST00000338382.11	Ensembl	ENSP00000344307.6	43	MANE Select
NM_001375568.1	RefSeq	NP_001362497.1	42	Standard
NM_001375570.1	RefSeq	NP_001362499.1	42	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

focal adhesion
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380249
Coding exons: 43
Length: 337647
Individuals with no LoFs: 125577
Homozygous LoFs: 0
Heterozygous LoFs: 171
Defined: 125748
p: 0.000680

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-2.93	1182	931	1.27	0.0000463	11679
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00069	0.00068	rare
Latino/Admixed American	0.00077	0.00075	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00029	0.00027	rare
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.00075	0.00072	rare
South Asian	0.0012	0.0012	notable
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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