SEC14L1

SEC14 like lipid binding 1, the group of SEC14 family|PRELI domain containing

Basic information

Region (hg38): 17:77088748-77217101

Previous symbols: [ "SEC14L" ]

Links

ENSG00000129657 ∙ NCBI:6397 ∙ OMIM:601504 ∙ HGNC:10698 ∙ Uniprot:Q92503 ∙ 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 SEC14L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC14L1 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				4	3	7
missense			31		2	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	31	4	5

Variants in SEC14L1

This is a list of pathogenic ClinVar variants found in the SEC14L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-77190839-C-G		Monoclonal B-Cell Lymphocytosis	Uncertain significance (Dec 15, 2015)
17-77190881-G-A		not specified	Uncertain significance (Jun 28, 2022)
17-77190913-C-G			Likely benign (Jan 01, 2023)
17-77191199-G-A		not specified	Uncertain significance (Nov 19, 2022)
17-77191278-A-G		not specified	Uncertain significance (Oct 22, 2021)
17-77191289-A-G		not specified	Uncertain significance (Jan 08, 2024)
17-77194716-G-C		not specified	Uncertain significance (Nov 14, 2023)
17-77194722-G-A		not specified	Uncertain significance (Dec 02, 2022)
17-77194821-G-A		not specified	Uncertain significance (Nov 16, 2021)
17-77194839-C-T		not specified	Uncertain significance (Oct 04, 2022)
17-77194864-C-T		not specified	Uncertain significance (Jan 19, 2024)
17-77196230-A-G			Benign (Jul 15, 2018)
17-77200572-C-T		not specified	Uncertain significance (Oct 05, 2021)
17-77200671-A-G		not specified	Uncertain significance (Nov 16, 2021)
17-77200679-G-A			Benign (Jul 15, 2018)
17-77203586-C-T			Benign (Jul 15, 2018)
17-77203637-G-A			Benign (Jul 15, 2018)
17-77203644-G-C		not specified	Uncertain significance (May 27, 2022)
17-77205307-G-A		not specified	Uncertain significance (Jan 23, 2023)
17-77205312-G-A		not specified	Uncertain significance (Dec 31, 2023)
17-77205324-A-G		not specified	Uncertain significance (Mar 24, 2023)
17-77206314-G-C		not specified	Uncertain significance (Dec 20, 2021)
17-77206373-C-T			Likely benign (Aug 05, 2018)
17-77206745-T-C			Likely benign (Aug 05, 2018)
17-77209351-C-A		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEC14L1	protein_coding	protein_coding	ENST00000392476	16	130382

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.633	0.367	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.43	294	437	0.672	0.0000264	4725
Missense in Polyphen		101	183.46	0.55051		2097
Synonymous	-0.555	187	178	1.05	0.0000119	1372
Loss of Function	4.54	8	38.3	0.209	0.00000181	444

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000793	0.0000791
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in innate immunity by inhibiting the antiviral RIG-I signaling pathway. In this pathway, functions as a negative regulator of DDX58/RIG-I, the cytoplasmic sensor of viral nucleic acids. Prevents the interaction of DDX58 with MAVS/IPS1, an important step in signal propagation (PubMed:23843640). May also regulate the SLC18A3 and SLC5A7 cholinergic transporters (PubMed:17092608). {ECO:0000269|PubMed:17092608, ECO:0000269|PubMed:23843640}.
• Pathway: Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway (Consensus)

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.681
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.4

Haploinsufficiency Scores

• pHI: 0.366
• hipred: Y
• hipred_score: 0.639
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.367

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sec14l1

Gene ontology

• Biological process: choline transport;negative regulation of RIG-I signaling pathway;innate immune response
• Cellular component: nucleoplasm;cytoplasm;Golgi apparatus;cytosol
• Molecular function: protein binding;RIG-I binding;molecular function regulator