CUX1

cut like homeobox 1, the group of CUT class homeoboxes and pseudogenes|Golgins

Basic information

Region (hg38): 7:101815904-102283958

Previous symbols: [ "CUTL1" ]

Links

ENSG00000257923 ∙ NCBI:1523 ∙ OMIM:116896 ∙ HGNC:2557 ∙ Uniprot:P39880, Q13948 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• global developmental delay with or without impaired intellectual development (Definitive), mode of inheritance: AD
• global developmental delay with or without impaired intellectual development (Strong), mode of inheritance: AD
• autosomal dominant non-syndromic intellectual disability (Supportive), mode of inheritance: AD
• global developmental delay with or without impaired intellectual development (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Global developmental delay with or without impaired intellectual development	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	30014507

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CUX1 gene.

• not_provided (206 variants)
• Inborn_genetic_diseases (153 variants)
• Global_developmental_delay_with_or_without_impaired_intellectual_development (89 variants)
• CUX1-related_disorder (30 variants)
• not_specified (17 variants)
• Duane_retraction_syndrome (3 variants)
• Neurodevelopmental_disorder (2 variants)
• See_cases (2 variants)
• Myeloproliferative_neoplasm (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CUX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000181552.4. 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	48	6	55
missense		2	287	36	1	326
nonsense	13	11	4			28
start loss						0
frameshift	4	13	7			24
splice donor/acceptor (+/-2bp)	1	4	10			15
Total	18	30	309	84	7

Highest pathogenic variant AF is 0.000006571511

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CUX1	protein_coding	protein_coding	ENST00000360264	24	468291

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.75	543	851	0.638	0.0000572	9753
Missense in Polyphen		4	20.007	0.19993		283
Synonymous	-0.541	396	383	1.04	0.0000285	3009
Loss of Function	7.25	6	72.7	0.0825	0.00000367	824

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.000163	0.000109
Finnish	0.0000472	0.0000462
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.000163	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in intra-Golgi retrograde transport. {ECO:0000269|PubMed:15718469}.
• Pathway: Disease;Vesicle-mediated transport;Membrane Trafficking;Intra-Golgi traffic;Signaling by FGFR in disease;Signaling by cytosolic FGFR1 fusion mutants;FGFR1 mutant receptor activation;Signaling by FGFR1 in disease;Diseases of signal transduction;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.449

Intolerance Scores

• loftool: 0.407
• rvis_EVS: -1.87
• rvis_percentile_EVS: 2.01

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.783

Gene Damage Prediction

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

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;retrograde transport, vesicle recycling within Golgi;regulation of transcription by RNA polymerase II;multicellular organism development;peptidyl-tyrosine phosphorylation;Golgi vesicle transport;positive regulation of dendrite morphogenesis
• Cellular component: Golgi membrane;nucleus;nucleoplasm;Golgi apparatus;cytosol
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;protein tyrosine kinase activity;protein binding, bridging;sequence-specific DNA binding