TECR

Chr 19AR

trans-2,3-enoyl-CoA reductase

Also known as: GPSN2, MRT14, SC2, TER

NCBI Gene: 9524ENSG00000099797UniProt: Q9NZ01

This gene encodes a multi-pass membrane protein that resides in the endoplasmic reticulum, and belongs to the steroid 5-alpha reductase family. The elongation of microsomal long and very long chain fatty acid consists of 4 sequential reactions. This protein catalyzes the final step, reducing trans-2,3-enoyl-CoA to saturated acyl-CoA. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Apr 2011]

Primary Disease Associations & Inheritance

Intellectual developmental disorder, autosomal recessive 14MIM #614020
AR
0
Active trials
14
Pathogenic / LP
78
ClinVar variants
8
Pubs (1 yr)
1.8
Missense Z
0.53
LOEUF
Clinical Summary— TECR
🧬
Gene-Disease Validity (ClinGen)
intellectual disability · ARLimited

Limited evidence — not for standalone diagnostic reporting

⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.27) despite low pLI — interpret in context.
📋
ClinVar Variants
14 Pathogenic / Likely Pathogenic· 41 VUS of 78 total submissions
📖
GeneReview available — TECR
Authoritative clinical overview · Recommended first read
Open GeneReview ↗
Some data sources returned errors (1)

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.53LOEUF
pLI 0.108
Z-score 3.21
OE 0.27 (0.15–0.53)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.78Z-score
OE missense 0.63 (0.54–0.74)
116 obs / 183.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.27 (0.15–0.53)
0≤0.351.4
Missense OE0.63 (0.54–0.74)
0≤0.61.4
Synonymous OE1.14
0≤1.21.6
LoF obs/exp: 6 / 22.4Missense obs/exp: 116 / 183.9Syn Z: -0.96
DNGOF
DN
0.74top 25%
GOF
0.6834th %ile
LOF
0.2777th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

78 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic13
Likely Pathogenic1
VUS41
Likely Benign17
Benign6
13
Pathogenic
1
Likely Pathogenic
41
VUS
17
Likely Benign
6
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
13
0
13
Likely Pathogenic
0
0
1
0
1
VUS
0
29
9
3
41
Likely Benign
0
0
6
11
17
Benign
0
0
2
4
6
Total029311878

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

View in ClinVar →

TECR · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 2 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients