Pilomatrixoma: genes and variants

Genes linked to Pilomatrixoma

• 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.

  8 disease-causing and 1 uncertain variants in CTNNB1 are linked to Pilomatrixoma.

• MUTYH: Adenine DNA glycosylase

  It removes adenines incorrectly paired with oxidized guanine, preventing characteristic G:C-to-T:A mutations during base-excision repair. Biallelic loss-of-function variants cause MUTYH-associated polyposis and substantially increase colorectal-cancer risk.

  1 disease-causing and 3 uncertain variants in MUTYH are linked to Pilomatrixoma.

Known disease-causing variants in Pilomatrixoma

Which prediction tools work for Pilomatrixoma

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

• AlphaMissense: 100 out of 100
• EVE: 100 out of 100
• PolyPhen-2: 99 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• SIFT: 94 out of 100
• CATVariant: 78 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• MutPred2: 60 out of 100 (learned from overlapping clinical labels, so this is optimistic)
• MetaLR: 41 out of 100 (learned from overlapping clinical labels, so this is optimistic)

Same protein, different disease

• Severe intellectual disability-progressive spastic diplegia syndrome is also caused by CTNNB1 variants; they fall mostly in different places as the Pilomatrixoma variants (5 disease-causing).
• Familial adenomatous polyposis is also caused by MUTYH variants; they fall mostly in different places as the Pilomatrixoma variants (27 disease-causing).
• Gastric cancer is also caused by MUTYH variants; they fall mostly in different places as the Pilomatrixoma variants (11 disease-causing).

Diseases related to Pilomatrixoma

• Colorectal cancer, also linked to CTNNB1 and MUTYH
• Ovarian cancer, also linked to CTNNB1
• Familial adenomatous polyposis, also linked to MUTYH
• Gastric cancer, also linked to MUTYH
• Malignant tumor of urinary bladder, also linked to CTNNB1
• Ovarian neoplasm, also linked to CTNNB1
• Carcinoma of colon, also linked to CTNNB1
• Hepatocellular carcinoma, also linked to CTNNB1
• Severe intellectual disability-progressive spastic diplegia syndrome, also linked to CTNNB1
• Medulloblastoma, also linked to CTNNB1
• Neoplasm of stomach, also linked to MUTYH
• Inherited polyposis and early onset colorectal cancer - germline testing, also linked to MUTYH

Frequently asked questions

Which genes are linked to Pilomatrixoma?

In CATVariant, Pilomatrixoma is linked to 2 analyzed proteins: CTNNB1 (Catenin beta-1) and MUTYH (Adenine DNA glycosylase).

How many genetic variants are linked to Pilomatrixoma?

20 variants: 9 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 4 are of uncertain significance or have conflicting reports.

Which uncertain variants in Pilomatrixoma 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 Pilomatrixoma?

Among tools not trained on clinical labels, AlphaMissense separates this disease's known disease-causing variants from harmless ones best (AUROC 1.00, based on 9 disease-causing and 68 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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