MSANTD3-TMEFF1

Chr 9

MSANTD3-TMEFF1 readthrough

Also known as: C9orf3-TMEFF1, C9orf30-TMEFF1

NCBI Gene: 100526694ENSG00000251349

The MSANTD3-TMEFF1 fusion protein combines DNA-binding domains from MSANTD3 with transmembrane and growth factor-like domains from TMEFF1 through naturally occurring read-through transcription. No pediatric neurological diseases have been definitively associated with mutations in this fusion transcript. The moderate loss-of-function intolerance scores (pLI 0.24, LOEUF 0.51) suggest some evolutionary constraint but do not indicate strong haploinsufficiency.

ResearchSummary from RefSeq
LOEUF 0.51
Clinical Summary— MSANTD3-TMEFF1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.24) despite low pLI — interpret in context.
📋
ClinVar Variants
33 unique Pathogenic / Likely Pathogenic· 30 VUS of 64 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.51LOEUF
pLI 0.237
Z-score 3.17
OE 0.24 (0.13–0.51)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.07Z-score
OE missense 0.78 (0.68–0.89)
142 obs / 182.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.24 (0.13–0.51)
0≤0.351.4
Missense OE0.78 (0.68–0.89)
0≤0.61.4
Synonymous OE0.98
0≤1.21.6
LoF obs/exp: 5 / 20.5Missense obs/exp: 142 / 182.7Syn Z: 0.12

ClinVar Variant Classifications

64 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic31
Likely Pathogenic2
VUS30
31
Pathogenic
2
Likely Pathogenic
30
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
31
0
31
Likely Pathogenic
0
0
2
0
2
VUS
0
27
3
0
30
Likely Benign
0
0
0
0
0
Benign
0
0
0
0
0
Total02736063

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

View in ClinVar →

Protein Context — Lollipop Plot

MSANTD3-TMEFF1 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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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