BEND4

protein-coding

BEN domain containing 4, the group of BEN domain containing

Gene summary

Predicted to enable DNA binding activity. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CCDC4

MANE transcript

NM_207406.4

Inheritance

—

ClinVar variants

U:108B:5

Top phenotype

Familial acute necrotizing encephalopathy

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr4:42,110,853-42,152,878

External References & Databases

Ensembl (ENSG00000188848)

Transcript & Mutation Effects

hg38 • Region Span ~42.0 kb

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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 BEND4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 108

not providedTotal: 6

Familial acute necrotizing encephalopathyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_207406.4. 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				2 clinvar		2
missense			107 clinvar	3 clinvar		110
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	108	5	0	113

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_207406.4	RefSeq	NP_997289.2	5	MANE Select
ENST00000502486.6	Ensembl	ENSP00000421169.1	5	MANE Select
NM_001159547.2	RefSeq	NP_001153019.1	5	Standard
ENST00000504360.5	Ensembl	ENSP00000421160.1	5	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000502486
Coding exons: 5
Length: 41941
Individuals with no LoFs: 124632
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 124638
p: 0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.10	180	227	0.794	0.0000125	3412
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.000035	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.146
RVIS EVS: 0.24
RVIS percentile EVS: 69.37

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.224

Gene Damage Prediction

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