BCLAF3

protein-coding

BCLAF1 and THRAP3 family member 3

Gene summary

Predicted to enable DNA binding activity and transcription coregulator activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nuclear speck. Predicted to be part of mediator complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CXorf23

MANE transcript

NM_001367774.2

Inheritance

—

ClinVar variants

U:161

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chrX:19,912,860-19,991,061

External References & Databases

Ensembl (ENSG00000173681)

Transcript & Mutation Effects

hg38 • Region Span ~78.2 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 BCLAF3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 7

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001367774.2. 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			23 clinvar			23
missense			95 clinvar			95
nonsense			14 clinvar			14
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			28 clinvar			28
Total	0	0	161	0	0	161

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 113 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001367774.2	RefSeq	NP_001354703.1	11	MANE Select
ENST00000379682.9	Ensembl	ENSP00000369004.4	11	MANE Select
NM_198279.4	RefSeq	NP_938020.2	11	Standard
ENST00000340625.3	Ensembl	ENSP00000342104.3	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379687
Coding exons: 11
Length: 57439
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.26	190	246	0.773	0.0000180	4521
Missense (PolyPhen)		29	58.193	0.49834		1175
Synonymous	0.502	77	82.8	0.930	0.00000596	1197
Loss of Function	3.70	5	25.0	0.200	0.00000201	459

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.07
RVIS percentile EVS: 48.54

Essentials

Essential (gene trap): N