Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_002834.4(PTPN11):c.1658C>T (p.Thr553Met)

CA134644

40570 (ClinVar)

Gene: PTPN11
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 8b509a72-e8ae-4215-92db-567fba446b08
Approved on: 2024-09-17
Published on: 2024-10-01

HGVS expressions

NM_002834.4:c.1658C>T
NM_002834.4(PTPN11):c.1658C>T (p.Thr553Met)
NC_000012.12:g.112502202C>T
CM000674.2:g.112502202C>T
NC_000012.11:g.112940006C>T
CM000674.1:g.112940006C>T
NC_000012.10:g.111424389C>T
NG_007459.1:g.88471C>T
ENST00000639857.2:c.1658C>T
ENST00000685487.1:c.*860C>T
ENST00000687120.1:n.1041C>T
ENST00000687906.1:c.1544C>T
ENST00000688597.1:c.1283C>T
ENST00000688701.1:n.902C>T
ENST00000690210.1:c.1658C>T
ENST00000690472.1:n.867C>T
ENST00000692624.1:c.*204C>T
ENST00000351677.7:c.1658C>T
ENST00000351677.6:c.1658C>T
ENST00000635625.1:c.1670C>T
NM_002834.3:c.1658C>T
NM_001330437.1:c.1670C>T
NM_001330437.2:c.1670C>T
NM_001374625.1:c.1655C>T
NM_002834.5:c.1658C>T
More

Benign

Met criteria codes 2
BP4 BA1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTPN11 Version 2.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The filtering allele frequency of the c.1658C>T (p.Thr553Met) variant in the PTPN11 gene (NM_002834.5(PTPN11):c.1658C>T (p.Thr553Met)) is 0.048% for European (Non-Finnish) chromosomes by the Exome Aggregation Consortium (49/66556 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1). Computational prediction tools and conservation analysis suggest that the p.Thr553Met variant does not impact the protein (BP4). In summary, this variant meets criteria to be classified as benign. RASopathy-specific ACMG/AMP criteria applied: BA1, BP4 (Version 2.1; 09/17/2024).
Met criteria codes
BP4
Computational prediction tools and conservation analysis suggest that the p.Thr553Met variant does not impact the protein (BP4)
BA1
The filtering allele frequency of the c.1658C>T (p.Thr553Met) variant in the PTPN11 gene is 0.048% for European (Non-Finnish) chromosomes by the Exome Aggregation Consortium (49/66556 with 95% CI), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert panel for autosomal dominant RASopathy variants (BA1).
Curation History
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