SEC13

Chr 3

SEC13 homolog, nuclear pore and COPII component

Also known as: D3S1231E, SEC13L1, SEC13R, npp-20

NCBI Gene: 6396ENSG00000157020UniProt: P55735

The protein encoded by this gene belongs to the SEC13 family of WD-repeat proteins. It is a constituent of the endoplasmic reticulum and the nuclear pore complex. It has similarity to the yeast SEC13 protein, which is required for vesicle biogenesis from endoplasmic reticulum during the transport of proteins. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Oct 2008]

115
ClinVar variants
43
Pathogenic / LP
0.02
pLI score
0
Active trials
Clinical Summary— SEC13
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.32) despite low pLI — interpret in context.
📋
ClinVar Variants
43 Pathogenic / Likely Pathogenic· 70 VUS of 115 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.
0.61LOEUF
pLI 0.018
Z-score 2.93
OE 0.32 (0.18–0.61)
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.
0.62Z-score
OE missense 0.88 (0.77–0.99)
172 obs / 196.5 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.0.32 (0.18–0.61)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.88 (0.77–0.99)
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.0.84
0≤1.21.6
LoF obs/exp: 7 / 21.7Missense obs/exp: 172 / 196.5Syn Z: 1.18

ClinVar Variant Classifications

115 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic40
Likely Pathogenic3
VUS70
Likely Benign2
40
Pathogenic
3
Likely Pathogenic
70
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
40
0
40
Likely Pathogenic
0
0
3
0
3
VUS
0
64
6
0
70
Likely Benign
0
1
0
1
2
Benign
0
0
0
0
0
Total065491115

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

View in ClinVar →

Protein Context — Lollipop Plot

SEC13 · 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
A Report of a Child with SEC31A-Related Neurodevelopmental Disorder.
AlTassan R et al.·Int J Mol Sci
2025Case report
COPII cage assembly factor Sec13 integrates information flow regulating endomembrane function in response to human variation.
Anglès F et al.·Sci Rep
2024
Gene profiling of SEC13, SMAD7, GHRL, long non-coding RNA GHRLOS, HIF-1α in gastric cancer patients.
Hussein NA et al.·Sci Rep
2022Cohort
Interdependence between Nuclear Pore Gatekeepers and Genome Caretakers: Cues from Genome Instability Syndromes.
Larizza L et al.·Int J Mol Sci
2024Review
Identification and validation of a glycolysis-related gene signature for depicting clinical characteristics and its relationship with tumor immunity in patients with colon cancer.
Liu G et al.·Aging (Albany NY)
2022Cohort
Latent trait modeling of tau neuropathology in progressive supranuclear palsy.
Kouri N et al.·Acta Neuropathol
2021Functional
Designing multi-epitope vaccines against Echinococcus granulosus: an in-silico study using immuno-informatics.
Khan J et al.·BMC Mol Cell Biol
2024
Enhanced mLST8 Expression Correlates with Tumor Progression in Hepatocellular Carcinoma.
Yu XN et al.·Ann Surg Oncol
2020
SEC23B is required for the maintenance of murine professional secretory tissues.
Tao J et al.·Proc Natl Acad Sci U S A
2012
Involvement of GATOR complex genes in familial focal epilepsies and focal cortical dysplasia.
Weckhuysen S et al.·Epilepsia
2016
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