TCEANC

Chr X

transcription elongation factor A N-terminal and central domain containing

Also known as: TCEANC1

NCBI Gene: 170082 ENSG00000176896 UniProt: Q8N8B7

This gene encodes a protein predicted to regulate transcription by RNA polymerase II in the nucleus. The gene shows tolerance to loss-of-function variants (pLI = 0.05, LOEUF = 1.07), and no established disease associations have been reported to date.

ResearchSummary from RefSeq

Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

ResearchGenerating clinical summary…

DNmechanismLOEUF 1.07

Clinical Summary— TCEANC

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Population Constraint (gnomAD)

Low constraint (pLI 0.05) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

36 VUS of 51 total submissions

Explore recent and relevant literature in Research Assistant →

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.07LOEUF

pLI 0.052

Z-score 1.46

OE 0.41 (0.19–1.07)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.28Z-score

OE missense 0.93 (0.79–1.09)

108 obs / 116.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.41 (0.19–1.07)

0≤0.351.4

Missense OE?0.93 (0.79–1.09)

0≤0.61.4

Synonymous OE?0.90

0≤1.21.6

LoF obs/exp: 3 / 7.2Missense obs/exp: 108 / 116.5Syn Z: 0.50

This gene — mechanism propensity

0.6648th %ile

GOF

0.5465th %ile

LOF

0.3164th %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

51 submitted variants in ClinVar

ClinVar

Classification Summary

VUS36

Likely Benign8

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	36	0	36
Likely Benign	7	1	8
Benign	0	0	0
Total	43	1	44

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

View in ClinVar →

76 pathogenic / likely-pathogenic (of 85) ClinVar copy-number / structural variants overlap TCEANC — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →