Sensorineural hearing loss disorder: genes and variants

Genes linked to Sensorineural hearing loss disorder

• FOXI1: Forkhead box protein I1

  It regulates genes needed for acid-base transport in kidney intercalated cells and ion homeostasis in the inner ear. Biallelic pathogenic variants can cause enlarged vestibular aqueduct with hearing loss, and disruption can also affect renal acidification.

  1 disease-causing and 1 uncertain variants in FOXI1 are linked to Sensorineural hearing loss disorder.

• SLC12A2: Solute carrier family 12 member 2

  It brings sodium, potassium, and chloride into cells and supports cell-volume control, epithelial secretion, and neuronal chloride homeostasis. Pathogenic variants can cause developmental disorders with hearing loss, growth abnormalities, or neurologic impairment.

  1 disease-causing and 0 uncertain variants in SLC12A2 are linked to Sensorineural hearing loss disorder.

• SLC26A4: Pendrin

  SLC26A4, known as pendrin, is an anion exchanger that transports chloride, iodide, and bicarbonate without directly using sodium. It supports ion balance in the inner ear and thyroid, and SLC26A4 variants cause Pendred syndrome and inherited deafness.

  1 disease-causing and 0 uncertain variants in SLC26A4 are linked to Sensorineural hearing loss disorder.

• USH2A: Usherin

  It helps organize extracellular and membrane structures required for cochlear hair-cell and photoreceptor function. Biallelic pathogenic variants cause Usher syndrome type 2A or nonsyndromic retinitis pigmentosa and can also produce isolated hearing loss.

  1 disease-causing and 0 uncertain variants in USH2A are linked to Sensorineural hearing loss disorder.

Weakly linked (only a few uncertain records): DBH, GJB2 and TECTA.

Known disease-causing variants in Sensorineural hearing loss disorder

Same protein, different disease

• Pendred syndrome is also caused by SLC26A4 variants; they fall mostly in different places as the Sensorineural hearing loss disorder variants (106 disease-causing).
• Autosomal recessive nonsyndromic hearing loss 4 is also caused by SLC26A4 variants; they fall mostly in different places as the Sensorineural hearing loss disorder variants (106 disease-causing).
• Rare genetic deafness is also caused by SLC26A4 variants; they fall mostly in different places as the Sensorineural hearing loss disorder variants (14 disease-causing).
• Monogenic hearing loss is also caused by SLC26A4 variants; they fall mostly in different places as the Sensorineural hearing loss disorder variants (6 disease-causing).
• Usher syndrome is also caused by USH2A variants; they fall mostly in different places as the Sensorineural hearing loss disorder variants (40 disease-causing).
• Retinitis pigmentosa is also caused by USH2A variants; they fall mostly in different places as the Sensorineural hearing loss disorder variants (23 disease-causing).

Diseases related to Sensorineural hearing loss disorder

• Autosomal recessive nonsyndromic hearing loss 4, also linked to FOXI1 and SLC26A4
• Pendred syndrome, also linked to FOXI1 and SLC26A4
• Rare genetic deafness, also linked to SLC26A4 and USH2A
• Hearing loss, also linked to SLC12A2 and SLC26A4
• Retinitis pigmentosa, also linked to USH2A
• RASopathy, also linked to SLC26A4
• Usher syndrome, also linked to USH2A
• Cone-rod dystrophy, also linked to USH2A
• Monogenic hearing loss, also linked to SLC26A4
• Retinal disorder, also linked to USH2A
• Deafness, also linked to SLC26A4
• Autosomal recessive retinitis pigmentosa, also linked to USH2A

Frequently asked questions

Which genes are linked to Sensorineural hearing loss disorder?

In CATVariant, Sensorineural hearing loss disorder is linked to 4 analyzed proteins: FOXI1 (Forkhead box protein I1), SLC12A2 (Solute carrier family 12 member 2), SLC26A4 (Pendrin) and USH2A (Usherin).

How many genetic variants are linked to Sensorineural hearing loss disorder?

8 variants: 4 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 Sensorineural hearing loss disorder 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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