SEC14L3

SEC14 like lipid binding 3, the group of SEC14 family

Basic information

Region (hg38): 22:30447959-30472017

Links

ENSG00000100012 ∙ NCBI:266629 ∙ OMIM:612824 ∙ HGNC:18655 ∙ Uniprot:Q9UDX4 ∙ 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 SEC14L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC14L3 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		1
missense			25			25
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	0

Variants in SEC14L3

This is a list of pathogenic ClinVar variants found in the SEC14L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-30460044-C-G		not specified	Uncertain significance (Mar 05, 2024)
22-30460054-C-T		not specified	Uncertain significance (Sep 01, 2021)
22-30460068-G-A		not specified	Uncertain significance (May 09, 2022)
22-30460077-C-A		not specified	Uncertain significance (Mar 08, 2024)
22-30461313-C-T		not specified	Uncertain significance (Sep 30, 2021)
22-30461369-C-T		not specified	Uncertain significance (Jan 31, 2024)
22-30461390-G-C		not specified	Uncertain significance (Dec 30, 2023)
22-30461406-G-A		not specified	Uncertain significance (Nov 14, 2023)
22-30461413-C-G		not specified	Uncertain significance (Dec 28, 2023)
22-30461419-C-A		not specified	Uncertain significance (Jan 31, 2022)
22-30461442-C-T		not specified	Uncertain significance (Jan 31, 2024)
22-30461562-C-T		not specified	Uncertain significance (Sep 01, 2021)
22-30461570-G-A		not specified	Uncertain significance (May 20, 2024)
22-30461609-C-T		not specified	Uncertain significance (May 13, 2024)
22-30461627-T-G		not specified	Uncertain significance (Sep 29, 2022)
22-30461654-C-T		not specified	Uncertain significance (Dec 11, 2023)
22-30461682-C-T		not specified	Uncertain significance (Feb 21, 2024)
22-30461687-T-C		not specified	Uncertain significance (Sep 21, 2023)
22-30462181-C-T		not specified	Uncertain significance (Jun 21, 2023)
22-30464846-G-C		not specified	Uncertain significance (Sep 22, 2023)
22-30466374-C-T			Likely benign (Jul 01, 2022)
22-30466385-G-A		not specified	Uncertain significance (Nov 08, 2021)
22-30468602-C-A		not specified	Uncertain significance (Aug 01, 2022)
22-30468612-C-A		not specified	Uncertain significance (Dec 15, 2022)
22-30468681-T-G		not specified	Uncertain significance (Apr 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC14L3	protein_coding	protein_coding	ENST00000215812	12	24091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.66e-23	0.0000796	125257	1	490	125748	0.00195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.263	231	243	0.952	0.0000141	2623
Missense in Polyphen		71	74.734	0.95004		854
Synonymous	0.814	85	95.1	0.894	0.00000589	740
Loss of Function	-1.04	31	25.3	1.22	0.00000130	280

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00227	0.00227
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.00169	0.00169
Finnish	0.00998	0.00998
European (Non-Finnish)	0.00119	0.00119
Middle Eastern	0.00169	0.00169
South Asian	0.00162	0.00160
Other	0.00196	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable hydrophobic ligand-binding protein; may play a role in the transport of hydrophobic ligands like tocopherol, squalene and phospholipids.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.762
• rvis_EVS: 1.16
• rvis_percentile_EVS: 92.59

Haploinsufficiency Scores

• pHI: 0.331
• hipred: N
• hipred_score: 0.248
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.116

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec14l3

Gene ontology

• Cellular component: extracellular exosome
• Molecular function: lipid binding