BLTP1

bridge-like lipid transfer protein family member 1, the group of bridge-like lipid transfer protein family

Basic information

Region (hg38): 4:122152331-122364167

Previous symbols: [ "KIAA1109" ]

Links

ENSG00000138688 ∙ NCBI:84162 ∙ OMIM:611565 ∙ HGNC:26953 ∙ Uniprot:Q2LD37 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Alkuraya-Kucinskas syndrome (Strong), mode of inheritance: AR
• Alkuraya-Kucinskas syndrome (Strong), mode of inheritance: AR
• Alkuraya-Kucinskas syndrome (Strong), mode of inheritance: AR
• Alkuraya-Kucinskas syndrome (Strong), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BLTP1 gene.

• Alkuraya-Kucinskas syndrome (8 variants)
• not provided (6 variants)
• 6 conditions (1 variants)
• Right aortic arch;Hemivertebrae;Renal agenesis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BLTP1 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			1	41	18	60
missense		4	246	9	8	267
nonsense	6	6				12
start loss						0
frameshift	8	1				9
inframe indel			3			3
splice donor/acceptor (+/-2bp)	1	8				9
splice region		1	5	5	3	14
non coding			4	3	88	95
Total	15	19	254	53	114

Highest pathogenic variant AF is 0.0000329

Variants in BLTP1

This is a list of pathogenic ClinVar variants found in the BLTP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-122170523-C-T			Benign (May 14, 2021)
4-122170662-G-A		BLTP1-related disorder	Likely benign (May 15, 2019)
4-122172862-C-T			Benign (May 13, 2021)
4-122173081-A-C		not specified	Uncertain significance (Aug 02, 2023)
4-122173086-C-T		Alkuraya-Kucinskas syndrome	Uncertain significance (Aug 26, 2022)
4-122173103-T-C		BLTP1-related disorder	Likely benign (Jan 28, 2023)
4-122173160-T-G		BLTP1-related disorder	Benign/Likely benign (Dec 31, 2019)
4-122174374-A-G			Benign (May 12, 2021)
4-122174548-C-T			Benign (May 12, 2021)
4-122174605-AG-A			Pathogenic (May 07, 2022)
4-122174620-A-G		BLTP1-related disorder	Likely benign (Mar 12, 2024)
4-122174642-A-G		not specified	Uncertain significance (Nov 15, 2021)
4-122174734-G-C			Benign (May 12, 2021)
4-122175683-C-T			Benign (May 12, 2021)
4-122175886-A-C		not specified	Uncertain significance (Jul 13, 2022)
4-122175895-C-A		not specified	Uncertain significance (Aug 28, 2023)
4-122186085-T-C		BLTP1-related disorder	Likely benign (Sep 06, 2019)
4-122186087-A-G		not specified	Uncertain significance (Jun 28, 2022)
4-122186105-A-G		not specified	Uncertain significance (Apr 12, 2023)
4-122186116-C-T		Alkuraya-Kucinskas syndrome	Uncertain significance (Dec 18, 2017)
4-122186149-A-G		not specified	Uncertain significance (Aug 01, 2022)
4-122186182-C-T			Uncertain significance (Oct 16, 2020)
4-122186189-T-C		not specified	Uncertain significance (Mar 17, 2022)
4-122187460-C-G		Alkuraya-Kucinskas syndrome • BLTP1-related disorder	Conflicting classifications of pathogenicity (Oct 19, 2020)
4-122187476-A-T		not specified	Uncertain significance (Feb 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BLTP1	protein_coding	protein_coding	ENST00000264501	84	210426

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.26e-21	1.00	124620	0	175	124795	0.000701

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	6.00	1707	2.56e+3	0.666	0.000130	32796
Missense in Polyphen		515	1106.4	0.46547		14192
Synonymous	1.47	816	871	0.937	0.0000428	9634
Loss of Function	9.56	84	246	0.342	0.0000137	3028

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00143	0.00143
Ashkenazi Jewish	0.000705	0.000695
East Asian	0.000619	0.000612
Finnish	0.000420	0.000417
European (Non-Finnish)	0.000795	0.000777
Middle Eastern	0.000619	0.000612
South Asian	0.000670	0.000654
Other	0.000998	0.000990

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.845
• rvis_EVS: -1.56
• rvis_percentile_EVS: 3.21

Haploinsufficiency Scores

• pHI: 0.425
• hipred: Y
• hipred_score: 0.685
• ghis: 0.629

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.249

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 4932438A13Rik
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: regulation of cell growth;regulation of epithelial cell differentiation;synaptic vesicle endocytosis
• Cellular component: nucleus;membrane;integral component of membrane;presynapse
• Molecular function: protein binding