Sensorineural hearing loss: genes and variants

Genes linked to Sensorineural hearing loss

• 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 ClinVar pathogenic / likely pathogenic and 1 uncertain variants in FOXI1 have source records linked to Sensorineural hearing loss. Association strength is not clinical gene validity.

• 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 ClinVar pathogenic / likely pathogenic and 0 uncertain variants in SLC12A2 have source records linked to Sensorineural hearing loss. Association strength is not clinical gene validity.

• 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 ClinVar pathogenic / likely pathogenic and 0 uncertain variants in SLC26A4 have source records linked to Sensorineural hearing loss. Association strength is not clinical gene validity.

• 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 ClinVar pathogenic / likely pathogenic and 0 uncertain variants in USH2A have source records linked to Sensorineural hearing loss. Association strength is not clinical gene validity.

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

ClinVar pathogenic and likely pathogenic variants linked to Sensorineural hearing loss

Same protein, different disease

• Pendred syndrome also has ClinVar records linked to SLC26A4 variants; they fall mostly in different places as the Sensorineural hearing loss variants (106 pathogenic / likely pathogenic).
• Autosomal recessive nonsyndromic hearing loss 4 also has ClinVar records linked to SLC26A4 variants; they fall mostly in different places as the Sensorineural hearing loss variants (106 pathogenic / likely pathogenic).
• Rare genetic deafness also has ClinVar records linked to SLC26A4 variants; they fall mostly in different places as the Sensorineural hearing loss variants (14 pathogenic / likely pathogenic).
• Monogenic hearing loss also has ClinVar records linked to SLC26A4 variants; they fall mostly in different places as the Sensorineural hearing loss variants (6 pathogenic / likely pathogenic).
• Usher syndrome also has ClinVar records linked to USH2A variants; they fall mostly in different places as the Sensorineural hearing loss variants (40 pathogenic / likely pathogenic).
• Retinitis pigmentosa also has ClinVar records linked to USH2A variants; they fall mostly in different places as the Sensorineural hearing loss variants (23 pathogenic / likely pathogenic).

Diseases related to Sensorineural hearing loss

• 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
• Autosomal recessive retinitis pigmentosa, also linked to USH2A
• Deafness, also linked to SLC26A4

Frequently asked questions

Which genes have records linked to Sensorineural hearing loss?

This view contains 4 analyzed proteins: FOXI1, SLC12A2, SLC26A4, USH2A. Links come from clinical records and association databases. They do not imply that every listed gene is a validated cause, and missing genes may not yet be analyzed.

What do the clinical classifications mean?

Linked records include 4 pathogenic or likely pathogenic variants, 2 variants of uncertain significance and 2 with conflicting classifications. Labels summarize source records; multi-condition records may not make a separate assertion for this disease. Check the original record and review status.

Does the evidence score change a VUS classification?

No. 0 VUS or conflicting variants reach the likely-pathogenic points range on the computable criteria available here. This is a research prioritization signal, not a clinical classification. Patient, family and other required evidence may be missing.

Can I download the variant evidence?

Download the CSV for all 8 variants in the selected disease scope, including clinical labels, review status, evidence criteria, predictor scores, functional measurements and population frequency where available.

About this data

Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from eligible public CATVariant analyses 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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