SHMT2

Chr 12AR

serine hydroxymethyltransferase 2

Also known as: GLYA, HEL-S-51e, NEDCASB, SHMT, mSHMT

This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on chromosome 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]

OMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalitiesMIM #619121
AR

Clinical highlights

Gene-disease validity (ClinGen)
neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormalities · ARLimitednot for standalone diagnostic reporting
0
Active trials
72
Pubs (1 yr)
P/LP submissions
P/LP missense
0.85
LOEUF
DN
Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
0.85LOEUF
pLI 0.000
Z-score 2.16
OE 0.56 (0.380.85)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
1.52Z-score
OE missense 0.76 (0.680.84)
234 obs / 309.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.56 (0.380.85)
00.351.4
Missense OE?0.76 (0.680.84)
00.61.4
Synonymous OE?1.08
01.21.6
LoF obs/exp: 16 / 28.4Missense obs/exp: 234 / 309.4Syn Z: -0.68

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SHMT2 · 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

No active trials found for this gene.

Search ClinicalTrials.gov →