MSX2

Chr 5

msh homeobox 2

Also known as: CRS2, FPP, HOX8, MSH, PFM, PFM1

This gene encodes a member of the muscle segment homeobox gene family. The encoded protein is a transcriptional repressor whose normal activity may establish a balance between survival and apoptosis of neural crest-derived cells required for proper craniofacial morphogenesis. The encoded protein may also have a role in promoting cell growth under certain conditions and may be an important target for the RAS signaling pathways. Mutations in this gene are associated with parietal foramina 1 and craniosynostosis type 2. [provided by RefSeq, Jul 2008]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtParietal foramina 1
UniProtParietal foramina with cleidocranial dysplasia
UniProtCraniosynostosis 2

Clinical highlights

Gene-disease validity (ClinGen)
parietal foramina · ADDefinitivesufficient evidence for diagnostic panels2 gene-disease associations curated in total
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
36
Pubs (1 yr)
P/LP submissions
P/LP missense
0.82
LOEUF
LOF
Mechanism· G2P
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GeneReview available — MSX2
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
0.82LOEUF
pLI 0.262
Z-score 1.90
OE 0.26 (0.100.82)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
0.47Z-score
OE missense 0.89 (0.781.03)
141 obs / 157.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.26 (0.100.82)
00.351.4
Missense OE?0.89 (0.781.03)
00.61.4
Synonymous OE?0.97
01.21.6
LoF obs/exp: 2 / 7.7Missense obs/exp: 141 / 157.6Syn Z: 0.18

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

MSX2 · 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.

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