BANF2

BANF family member 2

Basic information

Region (hg38): 20:17693672-17735871

Previous symbols: [ "C20orf179" ]

Links

ENSG00000125888 ∙ NCBI:140836 ∙ ∙ HGNC:16172 ∙ Uniprot:Q9H503 ∙ 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 BANF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BANF2 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in BANF2

This is a list of pathogenic ClinVar variants found in the BANF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-17725132-T-C		not specified	Uncertain significance (Aug 05, 2024)
20-17735697-G-A		not specified	Uncertain significance (Nov 10, 2022)
20-17735706-T-G		not specified	Uncertain significance (Dec 25, 2024)
20-17735767-C-A		not specified	Uncertain significance (Dec 27, 2023)
20-17735797-G-A		not specified	Uncertain significance (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BANF2	protein_coding	protein_coding	ENST00000545418	3	42200

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0143	0.695	125738	0	4	125742	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.419	44	52.6	0.837	0.00000259	640
Missense in Polyphen		18	17.913	1.0049		216
Synonymous	-0.482	24	21.2	1.13	0.00000122	174
Loss of Function	0.617	3	4.40	0.682	2.65e-7	46

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in BANF1 regulation and influence tissue-specific roles of BANF1.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.788
• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.89

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.111

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Banf2

Gene ontology

• Cellular component: nucleus;cytoplasm
• Molecular function: DNA binding