BLTP3B

protein-coding

bridge-like lipid transfer protein family member 3B, the group of bridge-like lipid transfer protein family

Gene summary

Enables GARP complex binding activity; lipid transfer activity; and protein homodimerization activity. Involved in early endosome to Golgi transport and intermembrane lipid transfer. Located in cytosol and early endosome. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

UHRF1BP1L

MANE transcript

NM_015054.2

Inheritance

—

ClinVar variants

U:172B:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr12:100,028,455-100,142,874

External References & Databases

Ensembl (ENSG00000111647)

Transcript & Mutation Effects

hg38 • Region Span ~114.4 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 BLTP3B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 163

not providedTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015054.2. 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			3 clinvar		7 clinvar	10
missense			162 clinvar	6 clinvar	5 clinvar	173
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	172	6	12	190

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015054.2	RefSeq	NP_055869.1	21	MANE Select
ENST00000279907.12	Ensembl	ENSP00000279907.7	21	MANE Select
NM_001006947.2	RefSeq	NP_001006948.1	13	Standard
ENST00000356828.7	Ensembl	ENSP00000349285.3	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
protein homodimerization activity
GARP complex binding

Cellular Component

early endosome
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000279907
Coding exons: 21
Length: 114394
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 66
Defined: 125744
p: 0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.10	645	729	0.885	0.0000349	9700
Missense (PolyPhen)		151	225.95	0.66828		3114
Synonymous	-0.887	270	252	1.07	0.0000122	2705
Loss of Function	5.29	17	61.9	0.275	0.00000299	839

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00083	0.00083	rare
European (Non-Finnish)	0.00026	0.00025	rare
South Asian	0.00017	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.640
RVIS EVS: 1.5
RVIS percentile EVS: 95.38

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.187

Gene Damage Prediction

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