Carcinoma of colon: genes and variants

Genes linked to Carcinoma of colon

• FGFR3: Fibroblast growth factor receptor 3

  It normally restrains growth-plate chondrocyte proliferation while regulating multiple developmental pathways. Activating germline variants cause achondroplasia and related skeletal dysplasias, while somatic activating alterations are common in bladder cancer and some other tumors.

  3 disease-causing and 0 uncertain variants in FGFR3 are linked to Carcinoma of colon.

• PIK3CA: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform

  Its p110-alpha catalytic activity generates PIP3 and activates AKT-dependent growth, survival, and metabolic signaling downstream of many receptors. Activating variants are frequent cancer drivers and, when present mosaically during development, can cause PIK3CA-related overgrowth spectrum.

  1 disease-causing and 0 uncertain variants in PIK3CA are linked to Carcinoma of colon.

• BRAF: Serine/threonine-protein kinase B-raf

  It relays activated RAS signals through MEK and ERK to control proliferation, differentiation, and survival. Activating variants, especially V600E, drive melanoma and several other cancers and create sensitivity to pathway-directed therapies.

  2 disease-causing and 0 uncertain variants in BRAF are linked to Carcinoma of colon.

• CTNNB1: Catenin beta-1

  It links cadherins to the cytoskeleton at adherens junctions and, when stabilized by Wnt signaling, enters the nucleus to regulate transcription. Activating somatic variants drive many cancers, while germline loss-of-function variants cause CTNNB1 neurodevelopmental disorder.

  1 disease-causing and 0 uncertain variants in CTNNB1 are linked to Carcinoma of colon.

• DCC: Netrin receptor DCC

  It guides developing axons in response to netrin signals and helps establish long-range neural connections across the midline. Heterozygous pathogenic variants can cause congenital mirror movements, while biallelic or severe variants can produce complex neurodevelopmental syndromes.

  1 disease-causing and 0 uncertain variants in DCC are linked to Carcinoma of colon.

• EP300: Histone acetyltransferase p300

  It acetylates histones and transcription factors and acts as a central coactivator for developmental and stress-responsive transcription. Germline loss-of-function variants cause Rubinstein-Taybi syndrome type 2, while acquired alterations occur in several cancers.

  1 disease-causing and 0 uncertain variants in EP300 are linked to Carcinoma of colon.

• PPARG: Peroxisome proliferator-activated receptor gamma

  It drives adipocyte differentiation, lipid storage, and insulin-sensitive metabolic programs in response to endogenous lipids and thiazolidinedione drugs. Dominant-negative variants cause familial partial lipodystrophy type 3 with severe insulin resistance and dyslipidemia.

  1 disease-causing and 0 uncertain variants in PPARG are linked to Carcinoma of colon.

Weakly linked (only a few uncertain records): BUB1B, FLCN, MLH1 and PALB2.

Known disease-causing variants in Carcinoma of colon

Which prediction tools work for Carcinoma of colon

How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).

• AlphaMissense: 84 out of 100
• MutPred2: 84 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• MetaLR: 83 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• CATVariant: 75 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• PolyPhen-2: 71 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• EVE: 70 out of 100
• SIFT: 69 out of 100

Same protein, different disease

• FGFR3-related chondrodysplasia is also caused by FGFR3 variants; they fall mostly in different places as the Carcinoma of colon variants (20 disease-causing).
• Hypochondroplasia is also caused by FGFR3 variants; they fall mostly in different places as the Carcinoma of colon variants (15 disease-causing).
• Achondroplasia is also caused by FGFR3 variants; they fall mostly in different places as the Carcinoma of colon variants (9 disease-causing).
• Thanatophoric dysplasia is also caused by FGFR3 variants; they fall mostly in different places as the Carcinoma of colon variants (8 disease-causing).
• Severe achondroplasia-developmental delay-acanthosis nigricans syndrome is also caused by FGFR3 variants; they fall mostly in different places as the Carcinoma of colon variants (5 disease-causing).
• RASopathy is also caused by BRAF variants; they fall mostly in different places as the Carcinoma of colon variants (36 disease-causing).
• Cardio-facio-cutaneous syndrome is also caused by BRAF variants; they fall mostly in different places as the Carcinoma of colon variants (26 disease-causing).
• Cardiofaciocutaneous syndrome is also caused by BRAF variants; they fall mostly in different places as the Carcinoma of colon variants (17 disease-causing).
• Noonan syndrome is also caused by BRAF variants; they fall mostly in different places as the Carcinoma of colon variants (11 disease-causing).
• Noonan syndrome and Noonan-related syndrome is also caused by BRAF variants; they fall mostly in different places as the Carcinoma of colon variants (10 disease-causing).
• PIK3CA related overgrowth syndrome is also caused by PIK3CA variants; they fall mostly in different places as the Carcinoma of colon variants (30 disease-causing).
• Cowden syndrome is also caused by PIK3CA variants; they fall mostly in different places as the Carcinoma of colon variants (23 disease-causing).
• Megalencephaly-capillary malformation-polymicrogyria syndrome is also caused by PIK3CA variants; they fall mostly in different places as the Carcinoma of colon variants (22 disease-causing).
• Ovarian neoplasm is also caused by PIK3CA variants; they fall mostly in different places as the Carcinoma of colon variants (5 disease-causing).
• PIK3CA constitutional syndrome is also caused by PIK3CA variants; they fall partly in the same places as the Carcinoma of colon variants (4 disease-causing).
• Pilomatrixoma is also caused by CTNNB1 variants; they fall partly in the same places as the Carcinoma of colon variants (8 disease-causing).
• Severe intellectual disability-progressive spastic diplegia syndrome is also caused by CTNNB1 variants; they fall mostly in different places as the Carcinoma of colon variants (5 disease-causing).
• Medulloblastoma is also caused by CTNNB1 variants; they fall in the same places as the Carcinoma of colon variants (4 disease-causing).
• Corpus callosum, agenesis of is also caused by DCC variants; they fall mostly in different places as the Carcinoma of colon variants (6 disease-causing).
• Rubinstein-Taybi syndrome due to EP300 haploinsufficiency is also caused by EP300 variants; they fall mostly in different places as the Carcinoma of colon variants (17 disease-causing).
• Menke-Hennekam syndrome is also caused by EP300 variants; they fall mostly in different places as the Carcinoma of colon variants (4 disease-causing).

Diseases related to Carcinoma of colon

• Colorectal cancer, also linked to BRAF, CTNNB1, EP300, FGFR3 and 1 more
• Malignant tumor of urinary bladder, also linked to CTNNB1, FGFR3 and PIK3CA
• Hepatocellular carcinoma, also linked to BRAF, CTNNB1 and PIK3CA
• Noonan syndrome, also linked to BRAF and PIK3CA
• Ovarian cancer, also linked to CTNNB1 and PIK3CA
• Non-small cell lung carcinoma, also linked to BRAF and PIK3CA
• Ovarian neoplasm, also linked to CTNNB1 and PIK3CA
• Lung cancer, also linked to BRAF and PIK3CA
• Renal cell carcinoma, also linked to BRAF and FGFR3
• Lip and oral cavity carcinoma, also linked to BRAF and PIK3CA
• Seborrheic keratosis, also linked to FGFR3 and PIK3CA
• Hypertrophic cardiomyopathy, also linked to BRAF

Frequently asked questions

Which genes are linked to Carcinoma of colon?

In CATVariant, Carcinoma of colon is linked to 7 analyzed proteins: FGFR3 (Fibroblast growth factor receptor 3), PIK3CA (Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform), BRAF (Serine/threonine-protein kinase B-raf), CTNNB1 (Catenin beta-1), DCC (Netrin receptor DCC), EP300 (Histone acetyltransferase p300) and 1 more.

How many genetic variants are linked to Carcinoma of colon?

16 variants: 10 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 6 are of uncertain significance or have conflicting reports.

Which uncertain variants in Carcinoma of colon look disease-causing?

None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.

Which variant effect predictor works best for Carcinoma of colon?

Among tools not trained on clinical labels, AlphaMissense separates this disease's known disease-causing variants from harmless ones best (AUROC 0.84, based on 9 disease-causing and 55 harmless variants).

About this data

Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.

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