GIGYF1

GRB10 interacting GYF protein 1, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 7:100679507-100694250

Previous symbols: [ "PERQ1" ]

Links

ENSG00000146830 ∙ NCBI:64599 ∙ OMIM:612064 ∙ HGNC:9126 ∙ Uniprot:O75420 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Strong), mode of inheritance: AD
• neurodevelopmental disorder (Moderate), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GIGYF1 gene.

• not_specified (162 variants)
• GIGYF1-related_disorder (42 variants)
• not_provided (13 variants)
• Neurodevelopmental_disorder (4 variants)
• Autism_spectrum_disorder (4 variants)
• GIGYF1-associated_neurodevelopmental_disorder (1 variants)
• GIGYF1-associated_disorder (1 variants)
• Coffin-Siris_syndrome_6 (1 variants)
• Neurodevelopmental_abnormality (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GIGYF1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001375765.1. 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				15	6	21
missense			156	5	3	164
nonsense		3	4			7
start loss						0
frameshift	6	3	7			16
splice donor/acceptor (+/-2bp)		1	2			3
Total	6	7	169	20	9

Highest pathogenic variant AF is 0.000045894

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GIGYF1	protein_coding	protein_coding	ENST00000275732	24	9942

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000342	1.00	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.149	656	645	1.02	0.0000450	6579
Missense in Polyphen		98	106.49	0.92031		1167
Synonymous	-3.44	352	279	1.26	0.0000195	2073
Loss of Function	4.93	22	64.9	0.339	0.00000364	636

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000250	0.000243
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000525	0.000508
European (Non-Finnish)	0.000219	0.000211
Middle Eastern	0.000109	0.000109
South Asian	0.000101	0.0000980
Other	0.000499	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act cooperatively with GRB10 to regulate tyrosine kinase receptor signaling. May increase IGF1 receptor phosphorylation under IGF1 stimulation as well as phosphorylation of IRS1 and SHC1 (By similarity). {ECO:0000250, ECO:0000269|PubMed:12771153}.

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.0883
• rvis_EVS: -1.66
• rvis_percentile_EVS: 2.75

Haploinsufficiency Scores

• pHI: 0.180
• hipred: Y
• hipred_score: 0.552
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.768

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gigyf1

Gene ontology

• Biological process: biological_process;insulin-like growth factor receptor signaling pathway
• Cellular component: protein-containing complex
• Molecular function: protein binding