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GeneBe

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

ENSG00000129657NCBI:6397OMIM:601504HGNC:10698Uniprot:Q92503AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC14L1 gene.

  • Inborn genetic diseases (23 variants)
  • not provided (11 variants)

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
clinvar
3
clinvar
7
missense
24
clinvar
2
clinvar
26
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 24 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)222961
17-77190881-G-A not specified Uncertain significance (Jun 28, 2022)2298195
17-77190913-C-G Likely benign (Jan 01, 2023)730749
17-77191199-G-A not specified Uncertain significance (Nov 19, 2022)2328516
17-77191278-A-G not specified Uncertain significance (Oct 22, 2021)2207579
17-77191289-A-G not specified Uncertain significance (Jan 08, 2024)2216620
17-77194716-G-C not specified Uncertain significance (Nov 14, 2023)3159113
17-77194722-G-A not specified Uncertain significance (Dec 02, 2022)2213343
17-77194821-G-A not specified Uncertain significance (Nov 16, 2021)2355316
17-77194839-C-T not specified Uncertain significance (Oct 04, 2022)2271260
17-77194864-C-T not specified Uncertain significance (Jan 19, 2024)3159114
17-77196230-A-G Benign (Jul 15, 2018)781390
17-77200572-C-T not specified Uncertain significance (Oct 05, 2021)2222344
17-77200671-A-G not specified Uncertain significance (Nov 16, 2021)2259308
17-77200679-G-A Benign (Jul 15, 2018)732021
17-77203586-C-T Benign (Jul 15, 2018)778750
17-77203637-G-A Benign (Jul 15, 2018)778751
17-77203644-G-C not specified Uncertain significance (May 27, 2022)2292025
17-77205307-G-A not specified Uncertain significance (Jan 23, 2023)3159108
17-77205312-G-A not specified Uncertain significance (Dec 31, 2023)3159109
17-77205324-A-G not specified Uncertain significance (Mar 24, 2023)2522934
17-77206314-G-C not specified Uncertain significance (Dec 20, 2021)2268486
17-77206373-C-T Likely benign (Aug 05, 2018)764140
17-77206745-T-C Likely benign (Aug 05, 2018)764141
17-77209351-C-A not specified Uncertain significance (Nov 08, 2022)2323772

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEC14L1protein_codingprotein_codingENST00000392476 16130382
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.6330.3671257300181257480.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.432944370.6720.00002644725
Missense in Polyphen101183.460.550512097
Synonymous-0.5551871781.050.00001191372
Loss of Function4.54838.30.2090.00000181444

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006160.0000615
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.0001850.000185
European (Non-Finnish)0.00007930.0000791
Middle Eastern0.0001090.000109
South Asian0.00006530.0000653
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sec14l1
Phenotype

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