NANOGNB

NANOG neighbor homeobox

Basic information

Region (hg38): 12:7765216-7774121

Links

ENSG00000205857 ∙ NCBI:360030 ∙ ∙ HGNC:24958 ∙ Uniprot:Q7Z5D8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NANOGNB 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						0
missense			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in NANOGNB

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

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

Position	Type	Phenotype	Significance	ClinVar
12-7765293-G-A		not specified	Uncertain significance (Feb 05, 2025)
12-7765322-G-A		not specified	Uncertain significance (Dec 15, 2023)
12-7765328-T-C		not specified	Uncertain significance (Jan 04, 2024)
12-7765332-A-G		not specified	Uncertain significance (Mar 20, 2023)
12-7765353-G-A		not specified	Uncertain significance (Jun 29, 2023)
12-7769989-T-A		not specified	Uncertain significance (Oct 21, 2024)
12-7770020-A-T		not specified	Uncertain significance (Nov 07, 2022)
12-7770193-G-A		not specified	Likely benign (Jun 11, 2021)
12-7770251-A-G		not specified	Uncertain significance (Sep 10, 2024)
12-7770263-C-T		not specified	Uncertain significance (Aug 28, 2023)
12-7770275-G-A		not specified	Uncertain significance (Aug 27, 2024)
12-7770299-A-G		not specified	Likely benign (Dec 20, 2023)
12-7770310-A-C		not specified	Uncertain significance (Nov 10, 2024)
12-7770467-A-G		not specified	Uncertain significance (Apr 10, 2023)
12-7770468-G-T		not specified	Uncertain significance (Nov 13, 2024)
12-7770475-A-G		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NANOGNB	protein_coding	protein_coding	ENST00000382119	4	8906

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00424	0.876	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.235	69	74.7	0.924	0.00000383	1223
Missense in Polyphen		13	14.284	0.91012		260
Synonymous	-0.846	34	28.3	1.20	0.00000169	303
Loss of Function	1.32	5	9.34	0.535	4.92e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Preimplantation Embryo (Consensus)

Intolerance Scores

• rvis_EVS: 0.81
• rvis_percentile_EVS: 87.76

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

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