BEND2

BEN domain containing 2, the group of BEN domain containing

Basic information

Region (hg38): X:18162930-18220886

Previous symbols: [ "CXorf20" ]

Links

ENSG00000177324 ∙ NCBI:139105 ∙ ∙ HGNC:28509 ∙ Uniprot:Q8NDZ0 ∙ 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 BEND2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEND2 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				3	1	4
missense			31	8	4	43
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	11	5

Variants in BEND2

This is a list of pathogenic ClinVar variants found in the BEND2 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-18165025-G-A		not specified	Uncertain significance (Apr 05, 2023)
X-18165029-C-T		not specified	Uncertain significance (Jan 09, 2024)
X-18165053-C-T		not specified	Uncertain significance (Mar 17, 2023)
X-18165057-C-T			Benign (Mar 29, 2018)
X-18165076-A-G		not specified	Uncertain significance (Aug 09, 2021)
X-18165091-T-C			Likely benign (Apr 01, 2023)
X-18165140-C-T		not specified	Likely benign (Dec 06, 2022)
X-18165187-G-A		not specified	Uncertain significance (May 14, 2024)
X-18171142-T-C		not specified	Likely benign (Jun 05, 2023)
X-18171168-G-A		not specified	Uncertain significance (Sep 15, 2021)
X-18171174-C-T		not specified	Likely benign (Oct 27, 2022)
X-18171190-G-A		not specified	Uncertain significance (Oct 13, 2023)
X-18174114-TC-T			Uncertain significance (Dec 14, 2015)
X-18174116-C-T		not specified	Uncertain significance (Jun 28, 2022)
X-18174117-T-A		not specified	Uncertain significance (Feb 12, 2024)
X-18174125-C-G		not specified	Uncertain significance (May 17, 2023)
X-18174129-T-G		not specified	Uncertain significance (Apr 26, 2024)
X-18174248-C-T		not specified	Uncertain significance (Aug 04, 2023)
X-18174249-G-A		not specified	Uncertain significance (Jul 08, 2022)
X-18175977-T-C		not specified	Uncertain significance (Jan 06, 2023)
X-18175985-C-A			Benign (Nov 18, 2017)
X-18176025-A-T		not specified	Uncertain significance (May 04, 2023)
X-18177592-G-A		not specified	Uncertain significance (Jun 06, 2023)
X-18177608-T-A		not specified	Uncertain significance (Jul 05, 2023)
X-18177615-C-A		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEND2	protein_coding	protein_coding	ENST00000380033	14	57974

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0885	0.911	124714	1	6	124721	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.713	257	291	0.882	0.0000218	5261
Missense in Polyphen		28	49.001	0.57142		982
Synonymous	-0.308	115	111	1.04	0.00000888	1534
Loss of Function	3.13	6	21.8	0.276	0.00000153	438

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000112	0.000112
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000791	0.0000545
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000791	0.0000545
South Asian	0.000179	0.000101
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0582

Intolerance Scores

• loftool: 0.444
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.18

Haploinsufficiency Scores

• pHI: 0.0457
• hipred: N
• hipred_score: 0.273

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00202

Gene Damage Prediction

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