FRYL

FRY like transcription coactivator, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 4:48497357-48780322

Previous symbols: [ "KIAA0826" ]

Links

ENSG00000075539 ∙ NCBI:285527 ∙ ∙ HGNC:29127 ∙ Uniprot:O94915 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Definitive), mode of inheritance: AD
• Pan-Chung-Bellen syndrome (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Pan-Chung-Bellen syndrome	AD	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic	38479391

ClinVar

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

• not_specified (244 variants)
• not_provided (79 variants)
• FRYL-related_developmental_disorder (14 variants)
• Pan-Chung-Bellen_syndrome (12 variants)
• FRYL-related_disorder (1 variants)
• See_cases (1 variants)
• FRYL-associated_neurodevelopmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FRYL gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015030.2. 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			1	6	3	10
missense			263	14	3	280
nonsense	2	2	5			9
start loss						0
frameshift	7	5	11			23
splice donor/acceptor (+/-2bp)		2	3			5
Total	9	9	283	20	6

Highest pathogenic variant AF is 0.0000020563832

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FRYL	protein_coding	protein_coding	ENST00000358350	61	282962

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00273	124753	0	43	124796	0.000172

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.96	1236	1.57e+3	0.790	0.0000812	19861
Missense in Polyphen		487	716.58	0.67962		9251
Synonymous	2.09	498	561	0.888	0.0000298	5690
Loss of Function	9.19	31	154	0.201	0.00000847	1906

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000534	0.000532
Ashkenazi Jewish	0.00	0.00
East Asian	0.000286	0.000278
Finnish	0.0000943	0.0000928
European (Non-Finnish)	0.000175	0.000168
Middle Eastern	0.000286	0.000278
South Asian	0.000104	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a key role in maintaining the integrity of polarized cell extensions during morphogenesis, regulates the actin cytoskeleton and plays a key role in patterning sensory neuron dendritic fields by promoting avoidance between homologous dendrites as well as by limiting dendritic branching (By similarity). May function as a transcriptional activator. {ECO:0000250, ECO:0000269|PubMed:16061630}.

Intolerance Scores

• loftool: 0.529
• rvis_EVS: -2.42
• rvis_percentile_EVS: 1.05

Haploinsufficiency Scores

• pHI: 0.220
• hipred: Y
• hipred_score: 0.685
• ghis: 0.621

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: E
• gene_indispensability_score: 0.892

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fryl
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); pigmentation phenotype; immune system phenotype; renal/urinary system phenotype

Zebrafish Information Network

• Gene name: fryl
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: malformed

Gene ontology

• Biological process: cell morphogenesis;neuron projection development
• Cellular component: cell cortex