TCEAL1

Chr XXLD

transcription elongation factor A like 1

Also known as: HIJRS, NEDGFAX, SIIR, WEX9, p21, pp21

TCEAL1 encodes a transcriptional regulator that modulates viral and cellular promoter activity in a context-dependent manner without directly binding DNA. Mutations cause Hijazi-Reis syndrome, an X-linked dominant disorder affecting neurological development. The gene shows moderate constraint against loss-of-function variants.

OMIMResearchSummary from OMIM, UniProt
DNmechanismXLDLOEUF 1.071 OMIM phenotype
Clinical SummaryTCEAL1
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.59) — some intolerance to loss-of-function variants.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
1.07LOEUF
pLI 0.586
Z-score 1.53
OE 0.00 (0.001.07)
Moderately constrained

Highly tolerant — LoF variants common in population

Missense Constraint
1.05Z-score
OE missense 0.61 (0.470.81)
35 obs / 57.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.00 (0.001.07)
00.351.4
Missense OE0.61 (0.470.81)
00.61.4
Synonymous OE1.01
01.21.6
LoF obs/exp: 0 / 2.7Missense obs/exp: 35 / 57.3Syn Z: -0.03
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
moderateTCEAL1-related neurodevelopmental disorderOTHERXLR
DN
0.6260th %ile
GOF
0.5953th %ile
LOF
0.4038th %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

TCEAL1 · 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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