TCEANC2

Chr 1

transcription elongation factor A N-terminal and central domain containing 2

Also known as: C1orf83

NCBI Gene: 127428 ENSG00000116205 UniProt: Q96MN5

The protein is predicted to regulate transcription by RNA polymerase II in the nucleus. This gene is not well-constrained against loss-of-function variants (LOEUF 1.666), and no established disease associations are documented in the provided data. Clinical significance of variants in TCEANC2 remains uncertain pending further characterization.

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 1.67

Clinical Summary— TCEANC2

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

20 VUS of 26 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.67LOEUF

pLI 0.000

Z-score -0.02

OE 1.01 (0.62–1.67)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.29Z-score

OE missense 0.92 (0.79–1.09)

107 obs / 115.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?1.01 (0.62–1.67)

0≤0.351.4

Missense OE?0.92 (0.79–1.09)

0≤0.61.4

Synonymous OE?0.88

0≤1.21.6

LoF obs/exp: 10 / 9.9Missense obs/exp: 107 / 115.7Syn Z: 0.65

This gene — mechanism propensity

0.6552th %ile

GOF

0.4972th %ile

LOF

0.3550th %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

26 submitted variants in ClinVar

ClinVar

Classification Summary

VUS20

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	20	20
Likely Benign	0	0
Benign	0	0
Total	20	20

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

View in ClinVar →

12 pathogenic / likely-pathogenic (of 16) ClinVar copy-number / structural variants overlap TCEANC2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →