BEND2

protein-coding

BEN domain containing 2, the group of BEN domain containing

Gene summary

This gene encodes a protein which has two BEN domains in the C-terminus. These domains are found in proteins which participate in protein and DNA interactions which occur during chromatin restructuring or transcription. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

Previous symbols:

CXorf20

MANE transcript

NM_153346.5

Inheritance

—

ClinVar variants

U:106B:22

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chrX:18,162,931-18,220,886

External References & Databases

Ensembl (ENSG00000177324)

Transcript & Mutation Effects

hg38 • Region Span ~58.0 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BEND2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 82

not providedTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153346.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			7 clinvar	3 clinvar	1 clinvar	11
missense			85 clinvar	14 clinvar	4 clinvar	103
nonsense			6 clinvar			6
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	106	17	5	128

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153346.5	RefSeq	NP_699177.2	14	MANE Select
ENST00000380033.9	Ensembl	ENSP00000369372.4	14	MANE Select
NM_001184767.2	RefSeq	NP_001171696.1	11	Standard
ENST00000380030.4	Ensembl	ENSP00000369369.3	11	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000380033
Coding exons: 14
Length: 57974
Individuals with no LoFs: 124714
Homozygous LoFs: 1
Heterozygous LoFs: 6
Defined: 124721
p: 0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.713	257	291	0.882	0.0000218	5261
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00011	0.000088	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000079	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.00018	0.00010	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0582

Intolerance Scores

LoFtool: 0.444
RVIS EVS: 0.69
RVIS percentile EVS: 85.18

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00202

Gene Damage Prediction

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