LDAF1

lipid droplet assembly factor 1

Basic information

Region (hg38): 16:21158377-21180616

Previous symbols: [ "TMEM159" ]

Links

ENSG00000011638 ∙ NCBI:57146 ∙ OMIM:611304 ∙ HGNC:30136 ∙ Uniprot:Q96B96 ∙ 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 LDAF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LDAF1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	8	0	0

Variants in LDAF1

This is a list of pathogenic ClinVar variants found in the LDAF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-21159340-T-A		not specified	Uncertain significance (Sep 16, 2021)
16-21159363-T-A		not specified	Uncertain significance (Jan 23, 2024)
16-21159374-C-A		not specified	Uncertain significance (Feb 03, 2022)
16-21159386-G-C		not specified	Uncertain significance (Dec 21, 2023)
16-21161213-A-G		not specified	Uncertain significance (Feb 28, 2023)
16-21170486-C-T		not specified	Uncertain significance (Dec 06, 2022)
16-21174078-G-A		not specified	Uncertain significance (Sep 28, 2021)
16-21174135-T-C		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LDAF1	protein_coding	protein_coding	ENST00000233047	4	22240

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00341	0.632	125709	0	38	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.523	74	87.8	0.843	0.00000440	1035
Missense in Polyphen		23	24.937	0.92232		321
Synonymous	0.278	35	37.2	0.942	0.00000217	332
Loss of Function	0.496	4	5.22	0.766	2.20e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000405	0.000405
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000158	0.000158
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000651	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.569
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.48

Haploinsufficiency Scores

• pHI: 0.0552
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0655

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tmem159

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: protein binding