NIBAN2

niban apoptosis regulator 2

Basic information

Region (hg38): 9:127505338-127578989

Previous symbols: [ "C9orf88", "FAM129B" ]

Links

ENSG00000136830 ∙ NCBI:64855 ∙ OMIM:614045 ∙ HGNC:25282 ∙ Uniprot:Q96TA1 ∙ 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 NIBAN2 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIBAN2 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				1		1
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	0

Variants in NIBAN2

This is a list of pathogenic ClinVar variants found in the NIBAN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-127506970-C-A		not specified	Uncertain significance (Jan 10, 2023)
9-127506999-G-A		not specified	Uncertain significance (Feb 06, 2023)
9-127507008-G-A		not specified	Uncertain significance (Nov 15, 2021)
9-127507027-C-T		not specified	Uncertain significance (Oct 27, 2022)
9-127507036-G-A		not specified	Uncertain significance (Jan 10, 2023)
9-127507135-T-C		not specified	Uncertain significance (Jan 04, 2024)
9-127507146-G-A		not specified	Uncertain significance (Nov 23, 2021)
9-127507155-G-A		not specified	Uncertain significance (Feb 05, 2024)
9-127507234-G-A		not specified	Uncertain significance (Nov 08, 2022)
9-127507236-C-T		not specified	Uncertain significance (Sep 22, 2022)
9-127507248-G-A		not specified	Uncertain significance (May 17, 2023)
9-127507297-C-T		not specified	Uncertain significance (Sep 17, 2021)
9-127507333-C-T		not specified	Uncertain significance (Jun 27, 2023)
9-127507414-C-G		not specified	Uncertain significance (Mar 01, 2024)
9-127507930-T-A		not specified	Uncertain significance (Jul 13, 2021)
9-127508149-G-C		not specified	Uncertain significance (Dec 13, 2023)
9-127508151-G-A		not specified	Uncertain significance (Oct 26, 2021)
9-127508194-C-T		not specified	Uncertain significance (Aug 12, 2021)
9-127508457-T-G		not specified	Uncertain significance (Aug 04, 2023)
9-127508523-C-T		not specified	Uncertain significance (Sep 22, 2022)
9-127509061-G-A		not specified	Uncertain significance (Mar 05, 2024)
9-127509076-T-C		not specified	Uncertain significance (Jun 14, 2022)
9-127509130-T-A		not specified	Uncertain significance (Sep 29, 2023)
9-127510166-C-T		not specified	Uncertain significance (Nov 01, 2022)
9-127510254-C-G		not specified	Uncertain significance (Jan 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIBAN2	protein_coding	protein_coding	ENST00000373312	14	73651

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0170	0.983	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.419	445	471	0.946	0.0000309	4835
Missense in Polyphen		129	159.39	0.80931		1595
Synonymous	0.688	206	219	0.941	0.0000161	1485
Loss of Function	4.44	12	43.6	0.275	0.00000273	408

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000359	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000252	0.000220
Middle Eastern	0.000359	0.000326
South Asian	0.000101	0.0000980
Other	0.000675	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in apoptosis suppression. May promote melanoma cell invasion in vitro. {ECO:0000269|PubMed:19362540, ECO:0000269|PubMed:21148485}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.717
• rvis_EVS: -1.35
• rvis_percentile_EVS: 4.63

Haploinsufficiency Scores

• pHI: 0.246
• hipred: Y
• hipred_score: 0.554
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam129b

Gene ontology

• Biological process: axon guidance;negative regulation of cell population proliferation;negative regulation of angiogenesis;cell differentiation;negative regulation of vascular endothelial growth factor receptor signaling pathway;gonadotropin secretion;positive regulation of embryonic development;negative regulation of apoptotic process;hypomethylation of CpG island;negative regulation of Notch signaling pathway;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of skeletal muscle fiber development;negative regulation of DNA biosynthetic process;positive regulation of transcription regulatory region DNA binding
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;adherens junction;extracellular exosome
• Molecular function: transcription coactivator activity;cadherin binding