NOBOX

NOBOX oogenesis homeobox, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 7:144397240-144410227

Links

ENSG00000106410 ∙ NCBI:135935 ∙ OMIM:610934 ∙ HGNC:22448 ∙ Uniprot:O60393 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• premature ovarian failure 5 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Premature ovarian failure 5	AD	Obstetric	Genetic knowledge may be beneficial to allow interventions such as preserving eggs in women with premature ovarian insufficiency	Endocrine; Obstetric	17701902; 21837770; 25514101

ClinVar

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

• not provided (3 variants)
• Premature ovarian failure 5 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOBOX 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			4	5	4	13
missense		1	67	5	9	82
nonsense	1	1				2
start loss						0
frameshift	2	1				3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			2	1	2	5
non coding			4	5	13	22
Total	3	3	75	15	26

Highest pathogenic variant AF is 0.00000657

Variants in NOBOX

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

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

Position	Type	Phenotype	Significance	ClinVar
7-144397272-T-C		Inborn genetic diseases	Uncertain significance (Nov 11, 2024)
7-144397274-G-GC		Genetic non-acquired premature ovarian failure	Pathogenic (Oct 01, 2019)
7-144397325-T-C		Premature ovarian failure 5 • not specified	Benign (Jan 12, 2018)
7-144397336-G-C		Premature ovarian failure 5	Uncertain significance (Jan 12, 2018)
7-144397355-G-A		Inborn genetic diseases	Uncertain significance (Feb 21, 2024)
7-144397368-C-T		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
7-144397378-T-C		Premature ovarian failure 5	Uncertain significance (Jan 13, 2018)
7-144397391-G-A		Inborn genetic diseases	Uncertain significance (Oct 25, 2023)
7-144397409-G-T		Inborn genetic diseases	Uncertain significance (Mar 11, 2024)
7-144397415-G-A			Uncertain significance (Jul 01, 2023)
7-144397416-G-T		Premature ovarian failure 5	Uncertain significance (Jan 13, 2018)
7-144397441-A-G		Premature ovarian failure 5	Uncertain significance (Jan 12, 2018)
7-144397460-G-A		Premature ovarian failure 5	Benign (Jan 13, 2018)
7-144397467-G-A		Premature ovarian failure 5	Uncertain significance (Jan 13, 2018)
7-144397469-C-T		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
7-144397486-G-C		Premature ovarian failure 5	Uncertain significance (Jan 15, 2018)
7-144397489-C-T		NOBOX-related disorder	Likely benign (Sep 06, 2019)
7-144397490-G-A		Premature ovarian failure 5 • Inborn genetic diseases	Conflicting classifications of pathogenicity (Apr 19, 2024)
7-144397513-C-A		Inborn genetic diseases	Uncertain significance (Aug 16, 2021)
7-144397520-G-T		Premature ovarian failure 5	Benign (Sep 05, 2021)
7-144397549-G-T		Premature ovarian failure 5	Benign (Dec 31, 2019)
7-144397625-C-T			Likely benign (May 20, 2019)
7-144397690-A-G			Benign (Jun 26, 2018)
7-144398264-C-T		not specified	Likely benign (Nov 13, 2017)
7-144398271-C-T		Premature ovarian failure 5	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOBOX	protein_coding	protein_coding	ENST00000467773	10	12988

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000206	0.995	124629	0	21	124650	0.0000842

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.481	358	385	0.931	0.0000208	4370
Missense in Polyphen		87	91.165	0.95431		1080
Synonymous	0.869	144	158	0.912	0.00000899	1461
Loss of Function	2.49	12	25.6	0.468	0.00000133	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000586	0.0000586
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000108	0.000106
Middle Eastern	0.000111	0.000111
South Asian	0.000167	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor which may play a role in oogenesis. Binds preferentially to the DNA sequences 5'-TAATTG-3', 5'-TAGTTG- 3' and 5'-TAATTA-3'. {ECO:0000269|PubMed:25514101, ECO:0000269|PubMed:27798098}.

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.423

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0290

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nobox
• 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); 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); embryo phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;multicellular organism development;oogenesis
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding