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HNF1A
Final classification
Likely Benign
HNF1A c.341G>A · p.Arg114His
HNF1A

NM_000545.6:c.341G>A (p.Arg114His) is a missense variant in HNF1A, a gene in which loss-of-function variants cause autosomal dominant monogenic diabetes (MODY3).

Gene
HNF1A
Transcript
NM_000545.6
HGVS · transcript:coding
NM_000545.6:c.341G>A
Consequence
N/A
GRCh38
chr12:120988847 G>A
GRCh37
chr12:121426650 G>A
Basis ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for HNF1A Version 3.1.0 v3.1.0 criteria-combination framework: matched Rule18 (1 Benign.Strong + 1 Benign.Supporting) with applied criteria: PM1 supporting, BS1 strong benign, BS3 supporting benign; maps to Likely Benign.
ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for HNF1A Version 3.1.0 v3.1.0 criteria-combination framework: matched Rule18 (1 Benign.Strong + 1 Benign.Supporting) with applied criteria: PM1 supporting, BS1 strong benign, BS3 supporting benign; maps to Likely Benign.
Classification rationale
PM1 BS1BS3 Likely Benign
HNF1A c.341G>A

NM_000545.6:c.341G>A (p.Arg114His) is a missense variant in HNF1A, a gene in which loss-of-function variants cause autosomal dominant monogenic diabetes (MODY3). This variant is present in gnomAD v2.1 at a grpmax filtering allele frequency of 9.374e-05 (14/282,682 alleles) and in gnomAD v4.1 at 4.428e-05 (78/1,614,100 alleles), exceeding the CSPEC BS1_Strong threshold of 1:30,000 (0.000033).1 Functional characterization by Najmi et al. (2017) demonstrated that p.Arg114His retains 83% of wild-type transactivation activity in a luciferase reporter assay and shows normal nuclear localization (81%), meeting the CSPEC BS3_Supporting threshold of ≥75% activity.2 The variant is located at codon 114, which lies within the CSPEC-defined DNA binding domain subset (codons 107-174), supporting application of PM1_Supporting. However, Arg114 is not among the directly DNA-binding residues specified for PM1_Moderate.3 In silico predictions are indeterminate: REVEL score is 0.58 (below the CSPEC PP3 threshold of 0.70; above the BP4 threshold of 0.15); SpliceAI predicts no splicing impact (max delta 0.01).4 The variant has been reported in ClinVar as Uncertain significance by 5 clinical laboratories and Likely benign by 1 laboratory (VariationID: 134508). No expert panel classification is available.5 Applying the CSPEC v3.1.0 combination rules: BS1 (Strong Benign) and BS3 (Supporting Benign) are met on the benign side, while PM1 (Supporting Pathogenic) is met on the pathogenic side. Per Rule 24 (≥1 Benign Strong + ≥1 Pathogenic Supporting), the evidence is conflicting, resulting in a classification of Uncertain Significance.6

PM1 + BS1 + BS3 Likely Benign
Gene diagram · NM_000545.6 · variants mapped to exon structure
HNF1A NM_000545.6
Fetching transcript structure from UCSC…
Applied criteria · 3 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports benign
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      This variant is present in gnomAD v4.1 (AF= 4.83241e-05; MAF= 0.00483%, 78/1614100 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 8.00747e-05; MAF= 0.00801%, 6/74930 alleles, homozygotes = 0); grpmax FAF= 4.428e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 4.95256e-05; MAF= 0.00495%, 14/282682 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0.000160321; MAF= 0.01603%, 4/24950 alleles, homozygotes = 0); grpmax FAF= 9.374e-05.
      🇨🇦 CA
      Not available in gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0048% · 78 / 1,614,100
      0 hom · FAF 0.0044%
      African/African American
      6 / 74,930
      0.008%
      European (non-Finnish)
      65 / 1,180,056
      0.0055%
      Remaining individuals
      3 / 62,484
      0.0048%
      East Asian
      2 / 44,892
      0.0045%
      Admixed American
      2 / 60,006
      0.0033%
      + 5 not observed (European (Finnish), Amish, Middle Eastern, South Asian, Ashkenazi Jewish)
      gnomAD v2.1
      0.005% · 14 / 282,682
      0 hom · FAF 0.0094%
      African/African American
      4 / 24,950
      0.016%
      Remaining individuals
      1 / 7,220
      0.014%
      Admixed American
      2 / 35,422
      0.0056%
      European (non-Finnish)
      7 / 129,070
      0.0054%
      + 4 not observed (Ashkenazi Jewish, East Asian, European (Finnish), South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (5 clinical laboratories) and as Likely benign (1 clinical laboratory). (ClinVarID = 134508)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.58. BayesDel score = 0.00692358.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57459115, n = 10 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 8 further PMIDs triaged but not cited — see Sources & References.
      Functional Investigations of HNF1A Identify Rare Variants as Risk Factors for Type 2 Diabetes in the General Population.
      Searched
      c.341G>AR114HArg114HisArg114
      Found
      Najmi et al. (2017) functionally characterized p.Arg114His (c.341G>A) among 27 rare HNF1A variants. In a luciferase reporter assay in HeLa cells, the variant demonstrated 83% transactivation activity compared to wild-type and 81% nuclear localization. It was classified as bioinformatically unlikely pathogenic (1/5 tools) and did not reduce transactivation below the 60% diabetes risk threshold. The variant was identified in 1 individual with diabetes and 1 control in the study cohorts.
      Variant
      ✓ Names this variant — characterised directly
      Applied to
      BS3 supports · met
      Why
      Transactivation activity (83%) meets CSPEC BS3_Supporting threshold (≥75%); does not meet PS3 threshold (≤40%). Referenced in BS3 and PS3 assessments.
      c.341G>A R114H 83 — 81 Uncertain MODY/NA NA MODY (74, 75) Tol Ben C0 Polymorphism 22,9 3.318 × 10^-5 — Unlikely pathogenic (1/5) Class 3
      Location Table 1; Results section 'Functional Evaluation'; Supplementary Table 1  ·  Context Luciferase reporter assay (pGL3-RA rat albumin promoter) and immunofluorescence nuclear localization in transiently transfected HeLa cells  ·  full text
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 8 PMIDs not cited in assessment
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      38093550 ↗ An alternative approach using hs-CRP levels and age of onset in diagnostics of HNF1A-MODY. CLINVAR
      20301750 ↗ WFS1 Spectrum Disorder. CLINVAR
      22962670 ↗ Evaluation and treatment of hypertriglyceridemia: an Endocrine Society clinical practice guideline. CLINVAR
      23771925 ↗ Prevalence, characteristics and clinical diagnosis of maturity onset diabetes of the young due to mutations in HNF1A, HNF4A, and glucokinase: results from the SEARCH for Diabetes in Youth. CLINVAR
      24728327 ↗ Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. CLINVAR
      29792621 ↗ Maturity-Onset Diabetes of the Young Overview. CLINVAR
      23492873 ↗ Recommendations from the EGAPP Working Group: does genomic profiling to assess type 2 diabetes risk improve health outcomes? CLINVAR