HERC1

Chr 15AR

HECT and RLD domain containing E3 ubiquitin protein ligase family member 1

This protein functions as a guanine nucleotide exchange factor for ARF1 and Rab proteins and may act as an E3 ubiquitin ligase, playing roles in membrane trafficking and clathrin binding. Biallelic mutations cause autosomal recessive macrocephaly, dysmorphic facies, and psychomotor retardation. The gene is highly constrained against loss-of-function variants (pLI ~1.0, LOEUF 0.24), indicating that heterozygous loss-of-function variants are likely not tolerated in the general population.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.241 OMIM phenotype
Clinical SummaryHERC1
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
Some data sources returned errors (1)

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.24LOEUF
pLI 1.000
Z-score 11.79
OE 0.19 (0.150.24)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
4.96Z-score
OE missense 0.72 (0.690.75)
1838 obs / 2541.0 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.19 (0.150.24)
00.351.4
Missense OE0.72 (0.690.75)
00.61.4
Synonymous OE1.02
01.21.6
LoF obs/exp: 46 / 245.4Missense obs/exp: 1838 / 2541.0Syn Z: -0.59
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveHERC1-related macrocephaly, dysmorphic facies, and psychomotor retardationLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.3097th %ile
GOF
0.2298th %ile
LOF
0.78top 5%

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

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

HERC1 · 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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