SUMO1

Chr 2Isolated cases

small ubiquitin like modifier 1

Also known as: DAP1, GMP1, OFC10, PIC1, SMT3, SMT3C, SMT3H3, UBL1

The protein functions as a small ubiquitin-like modifier that covalently attaches to target proteins to regulate nuclear transport, DNA replication and repair, transcriptional regulation, and signal transduction rather than targeting proteins for degradation. Pathogenic variants cause an autosomal recessive neurodevelopmental disorder characterized by intellectual disability, developmental delay, and cleft palate. The gene is highly constrained against loss-of-function variants in the population, indicating that such variants are likely to be pathogenic when present.

OMIMResearchSummary from RefSeq, UniProt
LOFmechanismIsolated casesLOEUF 0.461 OMIM phenotype
Clinical SummarySUMO1
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.86) — some intolerance to loss-of-function variants.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
0.46LOEUF
pLI 0.861
Z-score 2.36
OE 0.00 (0.000.46)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.51Z-score
OE missense 0.38 (0.260.57)
18 obs / 47.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.00 (0.000.46)
00.351.4
Missense OE0.38 (0.260.57)
00.61.4
Synonymous OE1.06
01.21.6
LoF obs/exp: 0 / 6.5Missense obs/exp: 18 / 47.1Syn Z: -0.19
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
limitedSUMO1-related cleft lip with or without cleft palateLOFAD
DN
0.3892th %ile
GOF
0.2895th %ile
LOF
0.75top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.46

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SUMO1 · 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

No active trials found for this gene.

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Clinical Literature
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