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 (Moderate), 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

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.

• Global developmental delay with or without impaired intellectual development (7 variants)
• Neurodevelopmental disorder (1 variants)
• Inborn genetic diseases (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				39	10	49
missense		1	153	29	4	187
nonsense	7	7	5			19
start loss						0
frameshift	1	11	7			19
inframe indel			6	1	1	8
splice donor/acceptor (+/-2bp)	1	4	1	1		7
splice region			5	4	4	13
non coding				1	7	8
Total	9	23	172	71	22

Variants in CUX1

This is a list of pathogenic ClinVar variants found in the CUX1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-101816042-T-C			Likely benign (Jun 13, 2018)
7-101816046-G-A		CUX1-related disorder	Uncertain significance (Sep 26, 2024)
7-101816068-A-G		Inborn genetic diseases	Uncertain significance (May 03, 2021)
7-101816091-C-T		Global developmental delay with or without impaired intellectual development	Likely pathogenic (Aug 31, 2018)
7-101816094-G-A		Intellectual disability • Global developmental delay with or without impaired intellectual development	Conflicting classifications of pathogenicity (Aug 03, 2020)
7-101816096-C-T		Inborn genetic diseases	Uncertain significance (Feb 12, 2021)
7-101817663-G-T			Uncertain significance (Jan 01, 2024)
7-101916137-C-T			Uncertain significance (Jul 06, 2022)
7-101916181-C-T		not specified	Uncertain significance (Jul 29, 2022)
7-101916207-C-G			Uncertain significance (Jan 29, 2024)
7-101916213-G-C		Inborn genetic diseases	Uncertain significance (Jun 01, 2023)
7-101916233-G-A		CUX1-related disorder	Benign (Dec 04, 2019)
7-102028117-C-G		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
7-102028118-G-A			Likely benign (Aug 01, 2024)
7-102070310-T-C		Global developmental delay with or without impaired intellectual development	Benign (Jul 30, 2021)
7-102070337-A-G		Global developmental delay with or without impaired intellectual development	Pathogenic (Dec 19, 2022)
7-102070339-A-G			Uncertain significance (May 26, 2023)
7-102070411-G-A		CUX1-related disorder	Benign/Likely benign (Aug 01, 2024)
7-102070418-G-A		Inborn genetic diseases	Likely pathogenic (Jan 19, 2022)
7-102097326-T-G		Global developmental delay with or without impaired intellectual development	Benign (Jul 30, 2021)
7-102097330-C-A		Global developmental delay with or without impaired intellectual development	Benign (Jul 30, 2021)
7-102097362-A-C		Inborn genetic diseases	Uncertain significance (Apr 04, 2024)
7-102097370-T-C		Global developmental delay with or without impaired intellectual development	Uncertain significance (Feb 06, 2020)
7-102097378-T-A			Uncertain significance (Jan 08, 2024)
7-102097381-G-C		Global developmental delay with or without impaired intellectual development	Uncertain significance (Sep 22, 2024)

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
1.00	5.47e-8	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

Haploinsufficiency Scores

• pHI: 0.784
• hipred: Y
• hipred_score: 0.792
• ghis: 0.506

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

Mouse Genome Informatics

• Gene name: Cux1
• Phenotype: skeleton phenotype; renal/urinary system phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); pigmentation phenotype; reproductive system 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); hematopoietic system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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); growth/size/body region phenotype

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