BLTP3A

protein-coding

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

Gene summary

Enables histone deacetylase binding activity and identical protein binding activity. Located in late endosome. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C6orf107
UHRF1BP1

MANE transcript

NM_017754.4

Inheritance

—

ClinVar variants

U:219B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr6:34,792,083-34,877,514

External References & Databases

Ensembl (ENSG00000065060)

Transcript & Mutation Effects

hg38 • Region Span ~85.4 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 BLTP3A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 205

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017754.4. 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			1 clinvar			1
missense			214 clinvar	7 clinvar	3 clinvar	224
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	219	7	3	229

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017754.4	RefSeq	NP_060224.3	21	MANE Select
ENST00000192788.6	Ensembl	ENSP00000192788.5	21	MANE Select
ENST00001115195.1	Ensembl	ENSP00000785000.1	15	Standard
ENST00001123360.1	Ensembl	ENSP00000793165.1	21	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
identical protein binding
histone deacetylase binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000192788
Coding exons: 21
Length: 91059
Individuals with no LoFs: 124674
Homozygous LoFs: 1
Heterozygous LoFs: 140
Defined: 124815
p: 0.000565

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.02	702	782	0.897	0.0000409	9434
Missense (PolyPhen)		190	226.98	0.83708		2770
Synonymous	1.07	267	290	0.920	0.0000141	2855
Loss of Function	3.93	32	66.6	0.480	0.00000360	741

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00019	rare
Latino/Admixed American	0.00052	0.00052	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00078	0.00078	rare
Finnish	0.0013	0.0013	notable
European (Non-Finnish)	0.00044	0.00044	rare
South Asian	0.00065	0.00062	rare
Other	0.00099	0.00099	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May act as a negative regulator of cell growth. {ECO:0000269|PubMed:15361834}.;

Recessive Scores

pRec: 0.0989

Intolerance Scores

LoFtool: 0.836
RVIS EVS: 0.44
RVIS percentile EVS: 77.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.627

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High