TECR

Chr 19AR

trans-2,3-enoyl-CoA reductase

Also known as: GPSN2, MRT14, SC2, TER

NCBI Gene: 9524 ENSG00000099797 UniProt: Q9NZ01 OMIM: 610057

TECR encodes an endoplasmic reticulum enzyme that catalyzes the final reduction step in very long-chain fatty acid elongation, converting trans-2,3-enoyl-CoA to saturated acyl-CoA for sphingolipid synthesis and membrane lipid production. Biallelic mutations cause autosomal recessive intellectual developmental disorder, also known as intellectual developmental disorder, autosomal recessive 14. This condition follows autosomal recessive inheritance and has a GeneReviews entry available for additional clinical guidance.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

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]

GeneReviews OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Intellectual developmental disorder, autosomal recessive 14MIM #614020

Clinical highlights

Gene–disease validity (ClinGen)

Limited · intellectual disability · AR · ClinGen 2022

not for standalone diagnostic reporting

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.53

LOEUF

Multiple*

Mechanism· predicted

📖

GeneReview available — TECR

Authoritative clinical overview · Recommended first read

Open GeneReview ↗

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 OE?0.27 (0.15–0.53)

0≤0.351.4

Missense OE?0.63 (0.54–0.74)

0≤0.61.4

Synonymous OE?1.14

0≤1.21.6

LoF obs/exp: 6 / 22.4Missense obs/exp: 116 / 183.9Syn Z: -0.96

Background carrier burden — how many people carry a rare variant somewhere in TECR?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 150

419 rare PASS variants

Rare truncating (LoF)

1 in 5,600

52 rare PASS variants

Rare synonymous (reference)

1 in 300

178 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for TECR. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 250	1 in 4,800
South Asian	~43k	1 in 190	≈ 1 in 21,000
Remaining (unassigned)	~30k	1 in 200	≈ 1 in 7,500
European (Finnish)	~27k	1 in 290	≈ 1 in 27,000
Admixed American	~22k	1 in 120	none seen
African / African American	~21k	1 in 200	none seen
East Asian	~20k	1 in 140	1 in 1,200
Ashkenazi Jewish	~13k	1 in 390	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 270	≈ 1 in 2,900

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 13 coding exons well covered in gnomAD exomes and genomes.? see exons ↓