SGMS2

Chr 4AD

sphingomyelin synthase 2

Also known as: CDL, SMS2

Sphingomyelin, a major component of cell and Golgi membranes, is made by the transfer of phosphocholine from phosphatidylcholine onto ceramide, with diacylglycerol as a side product. The protein encoded by this gene is an enzyme that catalyzes this reaction primarily at the cell membrane. The synthesis is reversible, and this enzyme can catalyze the reaction in either direction. The encoded protein is required for cell growth. Three transcript variants encoding the same protein have been found for this gene. There is evidence for more variants, but the full-length nature of their transcripts has not been determined.[provided by RefSeq, Oct 2008]

OMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Calvarial doughnut lesions with bone fragility with or without spondylometaphyseal dysplasiaMIM #126550
AD

Clinical highlights

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.
0
Active trials
16
Pubs (1 yr)
P/LP submissions
P/LP missense
0.58
LOEUF
Multiple*
Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint?
0.58LOEUF
pLI 0.057
Z-score 2.97
OE 0.29 (0.160.58)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?
1.10Z-score
OE missense 0.78 (0.690.89)
161 obs / 205.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.29 (0.160.58)
00.351.4
Missense OE?0.78 (0.690.89)
00.61.4
Synonymous OE?1.10
01.21.6
LoF obs/exp: 6 / 20.5Missense obs/exp: 161 / 205.3Syn Z: -0.65

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SGMS2 · 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 →