BEND4

BEN domain containing 4, the group of BEN domain containing

Basic information

Region (hg38): 4:42110853-42152878

Previous symbols: [ "CCDC4" ]

Links

ENSG00000188848 ∙ NCBI:389206 ∙ ∙ HGNC:23815 ∙ Uniprot:Q6ZU67 ∙ 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 BEND4 gene.

• not_specified (96 variants)
• not_provided (6 variants)
• Familial_acute_necrotizing_encephalopathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEND4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000207406.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			94	3		97
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	94	5	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BEND4	protein_coding	protein_coding	ENST00000502486	5	41941

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0152	124632	0	6	124638	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	180	227	0.794	0.0000125	3412
Missense in Polyphen		68	106.4	0.63908		1236
Synonymous	1.08	81	94.4	0.858	0.00000602	1065
Loss of Function	3.90	2	21.5	0.0929	0.00000133	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000994	0.0000994
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000359	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.0000350	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.146
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.404
• hipred: Y
• hipred_score: 0.672
• ghis: 0.441

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.224

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bend4