NIBAN3

niban apoptosis regulator 3

Basic information

Region (hg38): 19:17523301-17553839

Previous symbols: [ "FAM129C" ]

Links

ENSG00000167483 ∙ NCBI:199786 ∙ OMIM:609967 ∙ HGNC:24130 ∙ Uniprot:Q86XR2 ∙ 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 NIBAN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NIBAN3 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			64	5		69
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	65	5	0

Variants in NIBAN3

This is a list of pathogenic ClinVar variants found in the NIBAN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-17523451-C-G		not specified	Uncertain significance (Oct 20, 2023)
19-17523451-C-T		not specified	Uncertain significance (Sep 28, 2022)
19-17527285-G-A		not specified	Uncertain significance (Apr 24, 2023)
19-17527288-C-T		not specified	Uncertain significance (Nov 20, 2023)
19-17527341-A-T		not specified	Uncertain significance (Nov 08, 2024)
19-17527350-C-T		not specified	Uncertain significance (Aug 17, 2021)
19-17527373-G-C		not specified	Uncertain significance (Dec 08, 2023)
19-17527381-G-A		not specified	Likely benign (Sep 01, 2021)
19-17530773-T-A		not specified	Uncertain significance (Oct 27, 2022)
19-17530787-C-T		not specified	Uncertain significance (Feb 12, 2024)
19-17530836-G-A		not specified	Uncertain significance (Aug 05, 2024)
19-17530836-G-C		not specified	Uncertain significance (Jan 16, 2025)
19-17530877-C-T		not specified	Uncertain significance (Apr 06, 2024)
19-17530878-G-A		not specified	Likely benign (Feb 26, 2025)
19-17532265-G-T		not specified	Uncertain significance (Dec 05, 2024)
19-17532288-G-A		not specified	Uncertain significance (Feb 15, 2023)
19-17532308-C-T		not specified	Uncertain significance (Jun 03, 2022)
19-17532323-C-T		not specified	Uncertain significance (Nov 08, 2022)
19-17532353-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-17532363-G-A		not specified	Uncertain significance (Jan 31, 2023)
19-17532365-C-G		not specified	Uncertain significance (Jul 09, 2024)
19-17532368-G-C		not specified	Uncertain significance (Aug 28, 2024)
19-17533639-C-T		not specified	Uncertain significance (Mar 08, 2025)
19-17533657-G-T		not specified	Uncertain significance (Sep 07, 2022)
19-17533663-A-G		not specified	Uncertain significance (Apr 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NIBAN3	protein_coding	protein_coding	ENST00000335393	16	30539

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.24e-16	0.106	124463	22	1263	125748	0.00512

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.595	373	407	0.917	0.0000251	4341
Missense in Polyphen		112	128.32	0.87283		1472
Synonymous	1.12	158	177	0.893	0.0000108	1504
Loss of Function	1.05	28	34.7	0.808	0.00000194	353

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0278	0.0277
Ashkenazi Jewish	0.00209	0.00209
East Asian	0.0105	0.0105
Finnish	0.000647	0.000647
European (Non-Finnish)	0.000578	0.000563
Middle Eastern	0.0105	0.0105
South Asian	0.00174	0.00173
Other	0.00428	0.00424

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0841

Intolerance Scores

• loftool: 0.977
• rvis_EVS: 1.58
• rvis_percentile_EVS: 95.79

Haploinsufficiency Scores

• pHI: 0.0792
• hipred: N
• hipred_score: 0.153
• ghis: 0.387

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.325

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam129c