Seborrheic keratosis: genes and variants
Seborrheic keratosis is linked to 3 analyzed proteins (PIK3CA, FGFR3 and FLG). 1 DNA variants are known to cause it; 8 more are uncertain, and 0 of those already look disease-causing on computable evidence.
Last updated 2026-09-30. Research information, not medical advice.
Genes linked to Seborrheic keratosis
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 8 uncertain variants in PIK3CA are linked to Seborrheic keratosis.
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.
0 disease-causing and 0 uncertain variants in FGFR3 are linked to Seborrheic keratosis.
FLG: Filaggrin
It aggregates keratin fibers and is processed into natural moisturizing factors that are essential for epidermal barrier formation and hydration. Loss-of-function variants strongly predispose to ichthyosis vulgaris and atopic dermatitis by weakening the skin barrier.
0 disease-causing and 0 uncertain variants in FLG are linked to Seborrheic keratosis.
Known disease-causing variants in Seborrheic keratosis
| Variant | Position | Protein part | Clinical label |
|---|---|---|---|
| PIK3CA R38H | 38 | PI3K-ABD | Disease-causing (★★) |
Same protein, different disease
- PIK3CA related overgrowth syndrome is also caused by PIK3CA variants; they fall mostly in different places as the Seborrheic keratosis variants (30 disease-causing).
- Cowden syndrome is also caused by PIK3CA variants; they fall mostly in different places as the Seborrheic keratosis variants (23 disease-causing).
- Megalencephaly-capillary malformation-polymicrogyria syndrome is also caused by PIK3CA variants; they fall mostly in different places as the Seborrheic keratosis variants (22 disease-causing).
- Ovarian neoplasm is also caused by PIK3CA variants; they fall mostly in different places as the Seborrheic keratosis variants (5 disease-causing).
- PIK3CA constitutional syndrome is also caused by PIK3CA variants; they fall mostly in different places as the Seborrheic keratosis variants (4 disease-causing).
Diseases related to Seborrheic keratosis
- Colorectal cancer, also linked to FGFR3 and PIK3CA
- Malignant tumor of urinary bladder, also linked to FGFR3 and PIK3CA
- Carcinoma of colon, also linked to FGFR3 and PIK3CA
- Noonan syndrome, also linked to PIK3CA
- Cowden syndrome, also linked to PIK3CA
- Ovarian cancer, also linked to PIK3CA
- PIK3CA related overgrowth syndrome, also linked to PIK3CA
- Familial cancer of breast, also linked to PIK3CA
- Megalencephaly-capillary malformation-polymicrogyria syndrome, also linked to PIK3CA
- Connective tissue disorder, also linked to FGFR3
- FGFR3-related chondrodysplasia, also linked to FGFR3
- Gastric cancer, also linked to PIK3CA
Frequently asked questions
Which genes are linked to Seborrheic keratosis?
In CATVariant, Seborrheic keratosis is linked to 3 analyzed proteins: PIK3CA (Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform), FGFR3 (Fibroblast growth factor receptor 3) and FLG (Filaggrin).
How many genetic variants are linked to Seborrheic keratosis?
10 variants: 1 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 8 are of uncertain significance or have conflicting reports.
Which uncertain variants in Seborrheic keratosis look disease-causing?
None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.
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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