SEC14L2

Chr 22

SEC14 like lipid binding 2

Also known as: C22orf6, SPF, TAP, TAP1

NCBI Gene: 23541ENSG00000100003UniProt: O76054

This gene encodes a cytosolic protein which belongs to a family of lipid-binding proteins including Sec14p, alpha-tocopherol transfer protein, and cellular retinol-binding protein. The encoded protein stimulates squalene monooxygenase which is a downstream enzyme in the cholesterol biosynthetic pathway. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Oct 2008]

74
ClinVar variants
19
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— SEC14L2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
19 Pathogenic / Likely Pathogenic· 39 VUS of 74 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.94LOEUF
pLI 0.000
Z-score 1.81
OE 0.62 (0.42–0.94)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.99Z-score
OE missense 0.82 (0.72–0.92)
187 obs / 229.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.62 (0.42–0.94)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.82 (0.72–0.92)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.07
0≤1.21.6
LoF obs/exp: 16 / 25.9Missense obs/exp: 187 / 229.1Syn Z: -0.52

ClinVar Variant Classifications

74 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic18
Likely Pathogenic1
VUS39
Likely Benign2
Benign1
18
Pathogenic
1
Likely Pathogenic
39
VUS
2
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
18
0
18
Likely Pathogenic
0
0
1
0
1
VUS
0
36
3
0
39
Likely Benign
0
1
1
0
2
Benign
0
1
0
0
1
Total03823061

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

SEC14L2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Increased SEC14L2 expression is associated with clinicopathological features and worse prognosis in oral squamous cell carcinoma.
David JJ et al.·Odontology
2024
Identification of SEC14 like lipid binding 2(SEC14L2) sequence and expression profiles in the Chinese tree shrew (Tupaia belangeri chinensis).
Qiu D et al.·Mol Biol Rep
2022
SEC14L2, a lipid-binding protein, regulates HCV replication in culture with inter- and intra-genotype variations.
Costa R et al.·J Hepatol
2019
SEC14L2 enables pan-genotype HCV replication in cell culture.
Saeed M et al.·Nature
2015
Comprehensive analysis of cuproptosis-related genes and tumor microenvironment infiltration characterization in breast cancer.
Song S et al.·Front Immunol
2022
Identification of hub genes in AR-induced tamoxifen resistance in breast cancer based on weighted gene co-expression network analysis.
Lu C et al.·Breast Cancer Res Treat
2023
Association of variants in two vitamin e transport genes with circulating vitamin e concentrations and prostate cancer risk.
Wright ME et al.·Cancer Res
2009
Development and Validation of a Cholesterol-related Gene Signature for Prognostic Assessment in Head and Neck Squamous Cell Carcinoma.
Zheng J et al.·Curr Med Chem
2025
Expression Profile of Genes Regulating Steroid Biosynthesis and Metabolism in Human Ovarian Granulosa Cells-A Primary Culture Approach.
Kranc W et al.·Int J Mol Sci
2017
[Comparative Study of Diffuse Large B-Cell Lymphoma and Reactive Lymphoid Hyperplasia Lymph Node Derived Mesenchymal Stem Cells].
Ma YS et al.·Zhongguo Shi Yan Xue Ye Xue Za Zhi
2025
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools