TLCD3A

Chr 17

TLC domain containing 3A

Also known as: CT120, FAM57A

NCBI Gene: 79850ENSG00000167695UniProt: Q8TBR7

The protein encoded by this gene is a membrane-associated protein that promotes lung carcinogenesis. The encoded protein may be involved in amino acid transport and glutathione metabolism since it can interact with a solute carrier family member (SLC3A2) and an isoform of gamma-glutamyltranspeptidase-like 3. An alternatively spliced variant encoding a protein that lacks a 32 aa internal segment showed the opposite effect, inhibiting lung cancer cell growth. Knockdown of this gene also inhibited lung carcinogenesis and tumor cell growth. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2015]

170
ClinVar variants
61
Pathogenic / LP
0.26
pLI score
0
Active trials
Clinical Summary— TLCD3A
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.25) despite low pLI — interpret in context.
📋
ClinVar Variants
61 Pathogenic / Likely Pathogenic· 102 VUS of 170 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.65LOEUF
pLI 0.256
Z-score 2.40
OE 0.25 (0.11–0.65)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.22Z-score
OE missense 1.05 (0.92–1.21)
146 obs / 138.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.25 (0.11–0.65)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.05 (0.92–1.21)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.08
0≤1.21.6
LoF obs/exp: 3 / 11.9Missense obs/exp: 146 / 138.7Syn Z: -0.46

ClinVar Variant Classifications

170 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic55
Likely Pathogenic6
VUS102
Likely Benign7
55
Pathogenic
6
Likely Pathogenic
102
VUS
7
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
55
0
55
Likely Pathogenic
0
0
6
0
6
VUS
1
50
51
0
102
Likely Benign
0
5
2
0
7
Benign
0
0
0
0
0
Total1551140170

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

View in ClinVar →

Protein Context — Lollipop Plot

TLCD3A · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Identification of diagnostic biomarks and immune cell infiltration in ulcerative colitis.
Chen Q et al.·Sci Rep
2023
Molecular cloning and characterization of CT120, a novel membrane-associated gene involved in amino acid transport and glutathione metabolism.
He X et al.·Biochem Biophys Res Commun
2002
Silencing of CT120 by antisense oligonucleotides could inhibit the lung cancer cells growth.
Li Z et al.·Ir J Med Sci
2010
[Expression of human novel gene CT120 in lung cancer and its effects on cell growth].
He XH et al.·Ai Zheng
2003
Altered gene expression profiles of NIH3T3 cells regulated by human lung cancer associated gene CT120.
He XH et al.·Cell Res
2004
Inhibitory effect of CT120B, an alternative splice variant of CT120A, on lung cancer cell growth.
Pan DN et al.·Acta Biochim Biophys Sin (Shanghai)
2005
Parallel Reporter Assays Identify Altered Regulatory Role of rs684232 in Leading to Prostate Cancer Predisposition.
Ren N et al.·Int J Mol Sci
2021
Down-regulation of CT120A by RNA interference suppresses lung cancer cells growth and sensitizes to ultraviolet-induced apoptosis.
Pan D et al.·Cancer Lett
2006
[The effects of CT120B over-expression on growth suppression and changes of gene expression profiles in lung adenocarcinoma cells].
Pan DN et al.·Zhonghua Zhong Liu Za Zhi
2006
[Down-regulation of CT120A by RNA interference suppresses lung cancer cells growth].
Pan DN et al.·Zhonghua Yi Xue Za Zhi
2005
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools