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 (2 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. These statistics are base on transcript: . 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	4 clinvar	3 clinvar	10
missense		1 clinvar	78 clinvar	5 clinvar	9 clinvar	93
nonsense	1 clinvar	1 clinvar	1 clinvar			3
start loss						0
frameshift	3 clinvar	1 clinvar				4
splice donor/acceptor (+/-2bp)						0
Total	4	3	82	9	12

Highest pathogenic variant AF is 0.00000656909

Loading clinvar variants...

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

pHI
hipred: N
hipred_score: 0.123
ghis: 0.423

Essentials

essential_gene_CRISPR
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