BLTP3A

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

Basic information

Region (hg38): 6:34792082-34877514

Previous symbols: [ "C6orf107", "UHRF1BP1" ]

Links

ENSG00000065060 ∙ NCBI:54887 ∙ OMIM:619570 ∙ HGNC:21216 ∙ Uniprot:Q6BDS2 ∙ 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 BLTP3A gene.

• Inborn genetic diseases (24 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BLTP3A gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			23	1	3	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	3

Variants in BLTP3A

This is a list of pathogenic ClinVar variants found in the BLTP3A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-34821684-A-G		not specified	Uncertain significance (Oct 12, 2022)
6-34821780-A-G		not specified	Uncertain significance (Oct 05, 2023)
6-34821793-A-G		not specified	Uncertain significance (Jul 26, 2022)
6-34821951-G-C		not specified	Uncertain significance (Dec 21, 2022)
6-34823309-C-A		not specified	Uncertain significance (May 01, 2023)
6-34834228-T-A		not specified	Uncertain significance (Dec 26, 2023)
6-34834333-G-T			Benign (May 15, 2018)
6-34834351-A-G		not specified	Uncertain significance (Aug 02, 2021)
6-34834361-G-T		not specified	Uncertain significance (Feb 21, 2024)
6-34834380-C-T		not specified	Uncertain significance (Jul 20, 2021)
6-34834803-C-G		not specified	Uncertain significance (Aug 26, 2022)
6-34835393-G-A		not specified	Uncertain significance (Oct 18, 2021)
6-34835411-G-T		not specified	Uncertain significance (Jul 13, 2022)
6-34836162-C-T		not specified	Uncertain significance (Dec 08, 2023)
6-34836219-A-T		not specified	Uncertain significance (Mar 08, 2024)
6-34836241-G-A		not specified	Uncertain significance (Dec 28, 2023)
6-34836286-A-G		not specified	Uncertain significance (Feb 16, 2023)
6-34836339-C-G		not specified	Uncertain significance (Dec 20, 2023)
6-34855664-C-T		not specified	Uncertain significance (May 05, 2023)
6-34855700-G-T		not specified	Uncertain significance (Dec 04, 2023)
6-34856262-C-T		not specified	Uncertain significance (Aug 02, 2023)
6-34856286-C-G		not specified	Uncertain significance (Jan 10, 2022)
6-34856326-G-T		not specified	Uncertain significance (Dec 16, 2022)
6-34856353-C-T		not specified	Uncertain significance (Mar 06, 2023)
6-34856804-C-T		not specified	Uncertain significance (Aug 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BLTP3A	protein_coding	protein_coding	ENST00000192788	21	91059

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.47e-13	1.00	124674	1	140	124815	0.000565

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	702	782	0.897	0.0000409	9434
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000716	0.000715
Ashkenazi Jewish	0.000200	0.000199
East Asian	0.000779	0.000779
Finnish	0.00135	0.00135
European (Non-Finnish)	0.000443	0.000441
Middle Eastern	0.000779	0.000779
South Asian	0.000654	0.000621
Other	0.000991	0.000990

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.414
• ghis: 0.489

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.627

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Uhrf1bp1

Gene ontology

• Molecular function: protein binding;identical protein binding;histone deacetylase binding