What you carry at this position in your DNA and what research says about it.
Autoimmune Thyroid Risk: 8/10 evidence, 27 publications.
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Sample genotype (not yours): T/T
Typical Autoimmune Thyroid Risk
Standard thyroid function and a typical risk of autoimmune thyroid conditions are characteristic of this genetic profile. The absence of the low-frequency variant helps maintain normal immune cell signaling pathways. There is no elevated genetic predisposition to thyroid-related hormone imbalances.
What this genotype means: Typical baseline risk for autoimmune thyroiditis; Standard levels of circulating FLT3 ligand; Normal white blood cell and monocyte counts.
Sample genotype (not yours): C/C
Elevated Risk of Autoimmune Thyroid Disease
A significantly higher risk of autoimmune thyroid disease and hypothyroidism is linked to carrying two copies of this variant. The severe reduction in functional immune receptors triggers a major compensatory surge in inflammatory signaling proteins. This strongly predisposes the body to thyroid-directed autoimmune responses.
What this genotype means: Substantially elevated risk of autoimmune thyroid disease; Increased likelihood of requiring thyroid hormone therapy; Highly elevated circulating FLT3 ligand and monocyte levels.
Sample genotype (not yours): T/C
Increased Risk of Autoimmune Thyroid Disease
An increased risk of autoimmune thyroid disease and hypothyroidism is associated with this single-copy variant. A genetic alteration in immune receptor splicing leads to elevated levels of circulating immune-signaling proteins. This can prompt the immune system to mistakenly target the thyroid gland.
What this genotype means: Approximately 1.46x higher risk of autoimmune thyroid disease; Approximately 1.35x higher risk of hypothyroidism; Elevated levels of circulating FLT3 ligand and monocytes.
Gene function and biological role
Gene Function: The FLT3 gene encodes fms-related receptor tyrosine kinase 3, a cell-surface receptor crucial for the development and regulation of hematopoietic progenitor cells and dendritic cells [1]. It plays a vital role in the immune system by guiding the maturation of various white blood cells [1]. Under normal conditions, the FLT3 receptor binds to its specific signaling molecule, the FLT3 ligand, to control immune cell proliferation [2]. Disruptions in this pathway can alter immune tolerance and lead to autoimmune reactions [2].
Variant Impact: The rs76428106 variant is an intronic change in the FLT3 gene where the reference T allele is replaced by the C allele. This genetic change creates a cryptic splice site that introduces a premature stop codon in approximately 30% of the gene's transcripts [1]. The resulting truncated protein lacks the essential tyrosine kinase domains required for normal signaling [1]. To compensate for this loss of functional receptors, the body significantly increases the production of circulating FLT3 ligand [1] [2].
Key Insight: A genetic change that reduces functional immune receptors actually causes the body to overcompensate by doubling its circulating immune-signaling proteins.
Location: FLT3. Chromosome 13 · 13q12.2 · 28.0 Mb
Estimated prevalence by population
Global 98.0%; European 97.0%; African 99.5%; East Asian > 99.9%; South Asian 98.4%; Americas 97.8%; Ashkenazi 99.0%; Finnish 97.9%; Middle Eastern 99.3%; Amish 94.0%.
Estimated TT genotype frequency.
Global 2.0%; European 3.0%; African 0.5%; East Asian < 0.1%; South Asian 1.6%; Americas 2.2%; Ashkenazi 1.0%; Finnish 2.1%; Middle Eastern 0.7%; Amish 6.0%.
Estimated TC genotype frequency.
Global < 0.1%; European < 0.1%; African < 0.1%; East Asian < 0.1%; South Asian < 0.1%; Americas < 0.1%; Ashkenazi < 0.1%; Finnish < 0.1%; Middle Eastern < 0.1%; Amish 0.1%.
Estimated CC genotype frequency.
Showing effects for T/T genotype
Endocrine & Reproductive
Hormone Levels & Endocrine Regulation
Hypothyroidism. Evidence: 10/10. Source: PMID 30595370. Typical Risk.
Thyroid Medication Use. Evidence: 8/10. Source: PMID 31015401. Typical.
Immunity & Inflammation
Autoimmune Diseases
Autoimmune Thyroiditis. Evidence: 8/10. Source: PMID 32581359. Typical Risk.
Inflammatory & Circulating Protein Markers
FLT3 Ligand Levels. Evidence: 8/10. Source: PMID 32581359. Typical.
Cardiovascular & Metabolic
Blood Cell & Iron Traits
Monocyte Count. Evidence: 10/10. Source: PMID 27863252. Typical.
Lipids & Cholesterol
Total Cholesterol. Evidence: 10/10. Source: PMID 33462484. Typical.
Showing effects for C/C genotype
Hypothyroidism. Evidence: 10/10. Source: PMID 30595370. Elevated Risk.
Thyroid Medication Use. Evidence: 8/10. Source: PMID 31015401. Elevated Likelihood.
Autoimmune Thyroiditis. Evidence: 8/10. Source: PMID 32581359. Elevated Risk.
FLT3 Ligand Levels. Evidence: 8/10. Source: PMID 32581359. Significantly Higher.
Monocyte Count. Evidence: 10/10. Source: PMID 27863252. Significantly Higher.
Total Cholesterol. Evidence: 10/10. Source: PMID 33462484. Lower.
Showing effects for T/C genotype
Hypothyroidism. Evidence: 10/10. Source: PMID 30595370. ~1.35x Higher Risk.
Thyroid Medication Use. Evidence: 8/10. Source: PMID 31015401. Higher Likelihood.
Autoimmune Thyroiditis. Evidence: 8/10. Source: PMID 32581359. ~1.46x Higher Risk.
FLT3 Ligand Levels. Evidence: 8/10. Source: PMID 32581359. Higher.
Monocyte Count. Evidence: 10/10. Source: PMID 27863252. Higher.
Total Cholesterol. Evidence: 10/10. Source: PMID 33462484. Slightly Lower.
What this genotype means for the people who carry it
Sample genotype: TT (Homozygous)
Maintaining two copies of the common T allele ensures that the FLT3 gene undergoes normal splicing, producing fully functional receptors [1]. These receptors successfully regulate the development and maturation of dendritic cells and other key immune components [1]. Because immune signaling remains balanced, there is no compensatory surge in circulating FLT3 ligand levels [1] [2]. Consequently, the risk of developing autoimmune thyroid disease or requiring thyroid hormone replacement therapy remains at the baseline population level [3] [4]. Blood cell counts, including monocytes and lymphocytes, typically fall within standard reference ranges [1] [5]. Cholesterol levels also remain unaffected by this specific genetic locus [6]. Overall, this profile represents the most common and stable genetic baseline for thyroid and immune health.
Typical baseline risk for autoimmune thyroiditis; Standard levels of circulating FLT3 ligand; Normal white blood cell and monocyte counts.
Sample genotype: CC (Homozygous)
Possessing two copies of the C allele leads to a profound disruption in the splicing of the FLT3 gene [1]. With a majority of transcripts producing truncated, non-functional receptors, the normal regulation of immune cell development is severely altered [1]. The body responds with an intense compensatory increase in circulating FLT3 ligand levels to try to stimulate the remaining receptors [1] [2]. This dramatic imbalance heavily influences the behavior of dendritic cells and monocytes, significantly raising the risk of autoimmune thyroiditis [1] [3]. The likelihood of developing hypothyroidism and requiring daily thyroid hormone replacement is substantially elevated compared to the general population [3] [4]. Marked increases in white blood cell counts, particularly monocytes and lymphocytes, are commonly observed [5]. While this genotype strongly predisposes to autoimmune conditions, it is also associated with lower total cholesterol levels [6].
Substantially elevated risk of autoimmune thyroid disease; Increased likelihood of requiring thyroid hormone therapy; Highly elevated circulating FLT3 ligand and monocyte levels.
Sample genotype: TC (Heterozygous)
Carrying one copy of the C allele introduces a cryptic splice site that disrupts the normal production of the FLT3 receptor [1]. Approximately 30% of the transcripts from this gene are truncated, resulting in receptors that lack critical signaling domains [1]. To compensate for this deficiency, the body significantly increases the production of circulating FLT3 ligand, often doubling its plasma levels [1] [2]. This excess ligand alters the maturation and activity of dendritic cells and other white blood cells, increasing the likelihood of immune-mediated attacks on healthy tissues [1]. Clinical studies show a 1.46-fold increased risk of autoimmune thyroid disease and a 1.35-fold increased risk of hypothyroidism [1] [3]. This often manifests as a higher probability of needing thyroid hormone replacement medications [4]. Additionally, this profile is linked to higher circulating monocyte and lymphocyte counts [5]. Despite these immune changes, total cholesterol levels may be slightly lower [6].
Approximately 1.46x higher risk of autoimmune thyroid disease; Approximately 1.35x higher risk of hypothyroidism; Elevated levels of circulating FLT3 ligand and monocytes.
Variants with shared genetic architecture
rs1933437 · FLT3 Gene · Chr 13 · Blood Pressure and BMI
rs10849448 · LTBR Gene · Chr 12 · Respiratory Infection Risk
rs151234 · APOBR Gene · Chr 16 · Type 1 Diabetes Risk
FLT3 stop mutation increases FLT3 ligand level and risk of autoimmune thyroid disease.
A cross-population atlas of genetic associations for 220 human phenotypes.
Genome-wide association study of medication-use and associated disease in the UK Biobank.
A genetic map of human metabolism across the allele frequency spectrum.
Content updated August 2026.
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