TCEAL4

Chr X

transcription elongation factor A like 4

Also known as: NPD017, WEX7

NCBI Gene: 79921 ENSG00000133142 UniProt: Q96EI5 OMIM: 301154

The protein is a nuclear phosphoprotein that modulates transcription in a promoter context-dependent manner as part of the transcription elongation factor A (SII)-like gene family. Based on the provided information, there are no established disease associations or inheritance patterns documented for mutations in this gene. The moderate constraint scores suggest some intolerance to loss-of-function variants, but clinical significance remains to be determined.

OMIM ResearchSummary from RefSeq, UniProt

This gene encodes a member of the transcription elongation factor A (SII)-like (TCEAL) gene family. This family is comprised of nuclear phosphoproteins that modulate transcription in a promoter context-dependent manner. Multiple family members are located on the X chromosome. Alternatively splicing results in multiple transcript variants. There is a pseudogene for this gene on chromosome 13. [provided by RefSeq, Apr 2015]

OMIM ResearchGenerating clinical summary…

LOEUF 0.66

Clinical Summary— TCEAL4

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Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.75) — some intolerance to loss-of-function variants.

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ClinVar Variants

1 unique Pathogenic / Likely Pathogenic· 14 VUS of 38 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.66LOEUF

pLI 0.748

Z-score 1.98

OE 0.00 (0.00–0.66)

Moderately constrained

Typical tolerance to LoF variation

Missense Constraint?

0.95Z-score

OE missense 0.69 (0.55–0.87)

52 obs / 75.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.66)

0≤0.351.4

Missense OE?0.69 (0.55–0.87)

0≤0.61.4

Synonymous OE?1.08

0≤1.21.6

LoF obs/exp: 0 / 4.6Missense obs/exp: 52 / 75.3Syn Z: -0.31

ClinVar Variant Classifications

38 submitted variants in ClinVar

ClinVar

Classification Summary

Likely Pathogenic1

VUS14

Likely Benign4

Conflicting1

Likely Pathogenic

VUS

Likely Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	1	0	1
VUS	1	13	0	0	14
Likely Benign	0	2	0	2	4
Benign	0	0	0	0	0
Conflicting	—				1
Total	1	15	1	2	20

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

79 pathogenic / likely-pathogenic (of 87) ClinVar copy-number / structural variants overlap TCEAL4 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →