MTAP

Chr 9AD

methylthioadenosine phosphorylase

Also known as: BDMF, DMSFH, DMSMFH, HEL-249, LGMBF, MSAP, c86fus

The protein catalyzes the reversible phosphorylation of S-methyl-5'-thioadenosine to adenine and 5-methylthioribose-1-phosphate, functioning in polyamine metabolism and the methionine salvage pathway. Mutations cause diaphyseal medullary stenosis with malignant fibrous histiocytoma, inherited in an autosomal dominant pattern. The gene shows very low constraint against loss-of-function variants (pLI near zero), suggesting tolerance to such mutations in the general population.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismADLOEUF 1.391 OMIM phenotype
Clinical SummaryMTAP
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Gene-Disease Validity (ClinGen)
diaphyseal medullary stenosis-bone malignancy syndrome · ADModerate

Moderate evidence — consider for supplementary testing

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Clinical Trials
5 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
1.39LOEUF
pLI 0.000
Z-score 0.49
OE 0.86 (0.551.39)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.02Z-score
OE missense 1.00 (0.881.14)
167 obs / 166.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.86 (0.551.39)
00.351.4
Missense OE1.00 (0.881.14)
00.61.4
Synonymous OE1.25
01.21.6
LoF obs/exp: 12 / 14.0Missense obs/exp: 167 / 166.4Syn Z: -1.54
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
strongMTAP-related diaphyseal medullary stenosis with malignant fibrous histiocytomaLOFAD
DN
0.6455th %ile
GOF
0.5562th %ile
LOF
0.4332th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

MTAP · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
Clinical Literature
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