CRAMP1

Chr 16

cramped chromatin regulator 1

Also known as: CRAMP1L, HN1L, TCE4

NCBI Gene: 57585ENSG00000007545UniProt: Q96RY5

This protein is a transcription factor that drives expression of histone H1 genes by binding to their promoters together with NPAT and GON4L. The gene is highly constrained against loss-of-function variants (LOEUF 0.417), but no associated human disease has been reported to date. Clinical significance of variants in this gene remains to be established.

ResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.42
Clinical Summary— CRAMP1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.26) despite low pLI — interpret in context.
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.42LOEUF
pLI 0.050
Z-score 4.70
OE 0.26 (0.16–0.42)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.37Z-score
OE missense 0.86 (0.80–0.92)
607 obs / 709.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.26 (0.16–0.42)
0≤0.351.4
Missense OE0.86 (0.80–0.92)
0≤0.61.4
Synonymous OE1.11
0≤1.21.6
LoF obs/exp: 12 / 46.6Missense obs/exp: 607 / 709.7Syn Z: -1.57
DN
0.3495th %ile
GOF
0.3094th %ile
LOF
0.71top 10%

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

LOFprediction above median · LOEUF 0.42

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

ClinVar

Protein Context — Lollipop Plot

CRAMP1 · 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