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GeneBe

SEC14L2

SEC14 like lipid binding 2, the group of SEC14 family

Basic information

Region (hg38): 22:30396940-30425303

Previous symbols: [ "C22orf6" ]

Links

ENSG00000100003NCBI:23541OMIM:607558HGNC:10699Uniprot:O76054AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEC14L2 gene.

  • Inborn genetic diseases (6 variants)
  • not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEC14L2 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
6
clinvar
1
clinvar
7
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
Total 0 0 6 1 1

Variants in SEC14L2

This is a list of pathogenic ClinVar variants found in the SEC14L2 region.

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

Position Type Phenotype Significance ClinVar
22-30397150-C-G not specified Uncertain significance (Dec 28, 2023)3159118
22-30399716-G-A not specified Uncertain significance (Apr 17, 2023)2508429
22-30406381-G-A not specified Uncertain significance (Dec 21, 2023)3159115
22-30407108-G-A not specified Uncertain significance (Dec 17, 2023)3159116
22-30407128-A-G not specified Uncertain significance (Jan 09, 2024)3159117
22-30407568-C-A not specified Uncertain significance (Jan 02, 2024)3159119
22-30407590-A-G Benign (Jun 13, 2018)791373
22-30409214-A-G not specified Uncertain significance (Apr 12, 2022)2400221
22-30409259-C-G not specified Uncertain significance (Dec 20, 2023)3159120
22-30409292-A-T Likely benign (Aug 16, 2018)761094
22-30409454-C-A not specified Uncertain significance (Aug 05, 2023)2616561
22-30409456-G-A not specified Uncertain significance (Dec 01, 2022)2384097
22-30415794-C-T not specified Uncertain significance (Apr 24, 2023)2539836
22-30415803-G-A not specified Uncertain significance (Feb 02, 2022)2390132
22-30415957-G-A not specified Uncertain significance (Sep 23, 2023)3159121

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEC14L2protein_codingprotein_codingENST00000312932 1228460
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.92e-80.9191256990491257480.000195
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9891872290.8160.00001232640
Missense in Polyphen87118.040.737061327
Synonymous-0.5169487.81.070.00000465756
Loss of Function1.811625.90.6170.00000135284

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004960.000496
Ashkenazi Jewish0.000.00
East Asian0.0003260.000326
Finnish0.000.00
European (Non-Finnish)0.0001500.000149
Middle Eastern0.0003260.000326
South Asian0.0003270.000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Carrier protein. Binds to some hydrophobic molecules and promotes their transfer between the different cellular sites. Binds with high affinity to alpha-tocopherol. Also binds with a weaker affinity to other tocopherols and to tocotrienols. May have a transcriptional activatory activity via its association with alpha-tocopherol. Probably recognizes and binds some squalene structure, suggesting that it may regulate cholesterol biosynthesis by increasing the transfer of squalene to a metabolic active pool in the cell.;
Pathway
Validated transcriptional targets of deltaNp63 isoforms (Consensus)

Recessive Scores

pRec
0.126

Intolerance Scores

loftool
0.552
rvis_EVS
0.24
rvis_percentile_EVS
69.21

Haploinsufficiency Scores

pHI
0.280
hipred
N
hipred_score
0.396
ghis
0.486

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.223

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sec14l2
Phenotype
homeostasis/metabolism phenotype;

Gene ontology

Biological process
regulation of cholesterol biosynthetic process;positive regulation of transcription, DNA-templated
Cellular component
nucleus;cytoplasm;cytosol;extracellular exosome
Molecular function
phospholipid binding;vitamin E binding