NM_001098209.2:c.674G>A (p.Arg225His) is a missense variant in CTNNB1, present at extremely low frequency in population databases (gnomAD v2.1 AF=3.98e-06, v4.1 AF=1.86e-06), satisfying PM2 at supporting strength.1 This variant is classified as Uncertain Significance in ClinVar (ID 3257135) by two clinical laboratories with 1-star review status. It has been observed in COSMIC (n=4) in somatic cancers but lacks variant-specific functional characterization.2 Computational predictors do not support a deleterious effect: REVEL score 0.402, BayesDel -0.008, SpliceAI max delta 0.10. No functional studies, segregation data, or de novo reports are available for this variant.3 Only one criterion is met (PM2 at supporting strength). No pathogenic or benign criteria are satisfied. In accordance with ACMG/AMP 2015 combination rules, a single supporting pathogenic criterion with no opposing benign criteria results in a classification of Uncertain Significance.4
CTNNB1
Final classification
VUS
CTNNB1 c.674G>A · p.Arg225His
CTNNB1
NM_001098209.2:c.674G>A (p.Arg225His) is a missense variant in CTNNB1, present at extremely low frequency in population databases (gnomAD v2.1 AF=3.98e-06, v4.1 AF=1.86e-06), satisfying PM2 at supporting strength.
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; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2
VUS
CTNNB1 c.674G>A
PM2
→
VUS
Gene diagram
· NM_001098209.2 · variants mapped to exon structure
CTNNB1
NM_001098209.2
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 22 assessed
Applied · 1
Strength
Supporting
Moderate
Strong
Very strong
✓
PM2
supporting
Pathogenic
This variant is present at extremely low frequency in population databases: gnomAD v2.1 AF=3.98e-06 (1/251,024 alleles), gnomAD v4.1 AF=1.86e-06 (3/1,614,050 alleles), gnomAD v4.1 grpmax FAF=6.8e-07. All observed frequencies are well below the 0.1% PM2 threshold. No homozygotes reported.
gnomAD v2.1: 1/251024 (AF=3.98e-06)NFE AF=8.81e-06
Assessed · not applied
Pathogenic
PS1
No known pathogenic variant with the same amino acid change (p.Arg225His) at this position has been established in ClinVar or the literature.
PS2
No de novo occurrence reports were identified for this variant in the available literature or ClinVar submissions.
PS3
No variant-specific functional studies were identified.
PS4
No case-control studies or statistically significant enrichment of this variant in affected individuals versus controls has been reported.
PM1
Residue Arg225 is not located in a statistically significant mutational hotspot per cancerhotspots.org.
PM5
No pathogenic missense comparator variants at the same amino acid residue (Arg225) were identified.
PM6
No de novo occurrence of this variant has been reported in the available literature or ClinVar submissions.
PP1
No co-segregation data in affected families is available for this variant.
PP2
While CTNNB1 is associated with autosomal dominant neurodevelopmental disorder (CTNNB1 syndrome, MIM 615075) and loss-of-function is an established disease mechanism, PP2 requires demonstration of a low rate of benign missense variation in the gene (e.g., high missense Z-score).
PP3
In silico computational predictors do not support a deleterious effect: REVEL score 0.402 (below typical pathogenic threshold of 0.5), BayesDel score -0.008 (in benign range, below 0), and SpliceAI max delta score 0.10 (no predicted splicing impact, below 0.2 threshold).
PP4
No patient phenotype or clinical data were provided for this case.
PP5
ClinVar classifies this variant as Uncertain Significance (ClinVar ID 3257135) with review status 'criteria provided, single submitter' (1-star).
Benign
BA1
The maximum population allele frequency is 8.81e-06 in gnomAD v2.1 NFE, far below the BA1 threshold of >1%.
BS1
The maximum population allele frequency is 8.81e-06 in gnomAD v2.1 NFE, far below the BS1 threshold of >0.3%.
BS2
No homozygous observations in gnomAD (0 homozygotes in v2.1 and v4.1).
BS3
No well-established functional studies demonstrating a neutral or benign effect for p.Arg225His were identified.
BS4
No segregation data in affected families is available.
BP1
While the majority of CTNNB1 syndrome cases are caused by truncating variants, pathogenic missense variants in CTNNB1 are a recognized disease mechanism (PMID:33350591, PMID:36083290).
BP2
No evidence of this variant occurring in trans with a pathogenic CTNNB1 variant in any individual.
BP4
In silico predictors do not provide strong convergent evidence for a benign effect.
BP5
No alternate molecular basis for disease has been identified in this case.
BP6
ClinVar classifies this variant as Uncertain Significance, not benign.
N/A · 5
PVS1 · PM3 · PM4 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 1.85868e-06; MAF= 0.00019%, 3/1614050 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.54238e-06; MAF= 0.00025%, 3/1179996 alleles, homozygotes = 0); grpmax FAF= 6.8e-07.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.98368e-06; MAF= 0.00040%, 1/251024 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.81352e-06; MAF= 0.00088%, 1/113462 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00019%
· 3 / 1,614,050
0 hom · FAF 6.8e-05%
0 hom · FAF 6.8e-05%
European (non-Finnish) 3 / 1,179,996 |
0.00025% |
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0004%
· 1 / 251,024
0 hom
0 hom
European (non-Finnish) 1 / 113,462 |
0.00088% |
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 3257135)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.10). REVEL score = 0.402. BayesDel score = -0.00802185.
Functional
Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. CTNNB1 (β-catenin), a transcriptional activator, is recurrently mutated in various cancers including endometrial and hepatocellular cancers.
COSMIC
Cancer hotspots
Somatic evidence
Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV100846522, n = 4 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links