Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
PSEN1
Final classification
VUS
PSEN1 c.1234G>A · p.Val412Ile
PSEN1

NM_000021.3(PSEN1):c.1234G>A (p.Val412Ile) is extremely rare in population databases, with an allele frequency of 0.00107% in gnomAD v2.1 (3/280,740 alleles) and 0.00143% in gnomAD v4.1 (23/1,613,504 alleles), meeting PM2 at supporting level.

Gene
PSEN1
Transcript
NM_000021.3
HGVS · transcript:coding
NM_000021.3:c.1234G>A
Consequence
N/A
GRCh38
chr14:73217230 G>A
GRCh37
chr14:73683938 G>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, PP1 supporting; combination = 2 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM2 supporting, PP1 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM2PP1 VUS
PSEN1 c.1234G>A

NM_000021.3(PSEN1):c.1234G>A (p.Val412Ile) is extremely rare in population databases, with an allele frequency of 0.00107% in gnomAD v2.1 (3/280,740 alleles) and 0.00143% in gnomAD v4.1 (23/1,613,504 alleles), meeting PM2 at supporting level.1 The variant co-segregates with early-onset frontotemporal dementia in 4 affected individuals across 2 generations in the FUS family (Bernardi et al. 2009, PMID:18314228), meeting PP1 at supporting level. However, incomplete penetrance is noted with 2 cognitively healthy carriers identified at ages 49 and 71 in follow-up (Bernardi et al. 2011, PMID:21297264).2 No variant-specific functional data are available. The in vitro study of 138 PSEN1 pathogenic mutations by Sun et al. (PMID:27930341) did not include p.Val412Ile, as it is currently classified as a variant of uncertain significance.3 In silico predictors are mixed: REVEL score is 0.679, BayesDel is 0.305, and SpliceAI predicts no splicing impact (delta=0.00). The ClinVar submitter LabCorp notes 3 of 5 in silico tools predict a benign effect, precluding application of PP3.4 This variant is classified as Uncertain significance by 3 clinical laboratories in ClinVar (ID: 1318725). No submitter classifies it as pathogenic or likely pathogenic.5 Overall, the evidence for pathogenicity is limited to one supporting criterion (PM2) and one supporting criterion (PP1). With only 2 supporting criteria met and no moderate or strong pathogenic criteria, the variant does not reach the threshold for Likely Pathogenic (which requires 2 supporting + 1 moderate, or variants thereof). The classification remains Uncertain significance.6

PM2 + PP1 VUS
Gene diagram · NM_000021.3 · variants mapped to exon structure
PSEN1 NM_000021.3
Fetching transcript structure from UCSC…
Applied criteria · 2 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
      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= 1.42547e-05; MAF= 0.00143%, 23/1613504 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 6.67485e-05; MAF= 0.00667%, 5/74908 alleles, homozygotes = 0); grpmax FAF= 2.55e-05.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 1.0686e-05; MAF= 0.00107%, 3/280740 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 4.09802e-05; MAF= 0.00410%, 1/24402 alleles, homozygotes = 0); grpmax FAF= 2.95e-06.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0014% · 23 / 1,613,504
      0 hom · FAF 0.0026%
      African/African American
      5 / 74,908
      0.0067%
      South Asian
      2 / 91,082
      0.0022%
      Remaining individuals
      1 / 62,422
      0.0016%
      European (non-Finnish)
      15 / 1,179,924
      0.0013%
      + 6 not observed (Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish)
      gnomAD v2.1
      0.0011% · 3 / 280,740
      0 hom · FAF 0.0003%
      African/African American
      1 / 24,402
      0.0041%
      European (non-Finnish)
      2 / 128,152
      0.0016%
      + 6 not observed (Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, 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 (3 clinical laboratories). (ClinVarID = 1318725)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.679. BayesDel score = 0.305405.
      Functional No data
      No calibrated functional assay or RNA evidence was identified for this variant.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Literature · how each cited paper was used
      2papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 3 further PMIDs triaged but not cited — see Sources & References.
      Novel PSEN1 and PGRN mutations in early-onset familial frontotemporal dementia.
      Searched
      c.1234G>Ap.Val412IleV412IVal412Ilec.1234
      Found
      Identified PSEN1 Val412Ile as a novel heterozygous mutation in an autosomal dominant early-onset frontotemporal dementia family (FUS pedigree). The proband, a 38-year-old female, developed progressive mood and personality changes at age 30 with subsequent cognitive decline, mutism, myoclonus, and seizures. Four affected individuals across two generations carried the mutation. Mutation was absent from 100 cognitively healthy controls and 100 previously screened familial Alzheimer disease patients.
      Variant
      ✓ Names this variant — characterised directly
      Applied to
      PP1 supports · met
      Why
      Variant confirmed in affected family cohort; segregation data support PP1 at supporting level despite incomplete penetrance noted in follow-up study.
      Val412Ile is a heterozygous transition in exon 11 (g.69148G>A according to GenBank accession number AF109907.1; c.1234 according to GenBank accession number NM 000021.2) of the PSEN1 gene in the first position of codon 412, which predicts an aminoacidic substitution from valine to isoleucine and it was detected in a 38-year-old female (FUS family).
      Location Abstract; Results, sections 3.1-3.2; Figure 2; Figure 3A pedigree; Discussion  ·  Context DHPLC screening and Sanger sequencing of PSEN1 exons 3-12 in 17 f-EOFTD patients; RFLP and DHPLC for control validation  ·  full text
      PSEN1 and PRNP gene mutations: co-occurrence makes onset very early in a family with FTD phenotype.
      Searched
      c.1234G>Ap.Val412IleV412IVal412Ilec.1234
      Found
      Follow-up study of the FUS family originally reported in Bernardi et al. 2009. Identified a novel seven extra-repeat PRNP insertional mutation co-occurring with PSEN1 Val412Ile. PSEN1 Val412Ile alone was found in 2 affected and 2 cognitively healthy carriers (ages 49 and 71), demonstrating incomplete penetrance. Double carriers (PSEN1 + PRNP) had very early onset within the third decade. Both mutations showed variable penetrance when present separately.
      Variant
      ✓ Names this variant — characterised directly
      Applied to
      PP1 supports · met
      Why
      Documented incomplete penetrance (2 healthy carriers at ages 49 and 71) which tempers PP1 segregation evidence. Co-occurring PRNP mutation does not explain all affected cases, so BP5 not met.
      The PSEN1 Val412Ile mutation, which was previously detected in the three patients [14], was also identified in two additional family members (IV-5, III-2, in this paper).
      Location Abstract; Results; Table 1; Figure 1 pedigree; Discussion  ·  Context Bidirectional sequencing of PRNP and PSEN1 genes; APOE genotyping, MAPT haplotype analysis, PRNP M129V polymorphism assessment  ·  full text
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 3 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
      27930341 ↗ Analysis of 138 pathogenic mutations in presenilin-1 on the in vitro production of Aβ42 and Aβ40 peptides by γ-secretase. CLINVAR
      29091718 ↗ Analysis of neurodegenerative Mendelian genes in clinically diagnosed Alzheimer Disease. CLINVAR