The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000314.8(PTEN):c.30_32del (p.Ser10del)

CA645369491

428224 (ClinVar)

Gene: PTEN (HGNC:5728)
Condition: PTEN hamartoma tumor syndrome (MONDO:0017623)
Inheritance Mode: Autosomal dominant inheritance
UUID: c5f9e697-a1e8-4332-aa58-6954a9570db6
Approved on: 2026-06-16
Published on: 2026-06-26

HGVS expressions

NM_000314.8(PTEN):c.30_32del (p.Ser10del)
NM_000314.8:c.30_32del
NC_000010.11:g.87864499_87864501del
CM000672.2:g.87864499_87864501del
NC_000010.10:g.89624256_89624258del
CM000672.1:g.89624256_89624258del
NC_000010.9:g.89614236_89614238del
NG_007466.2:g.6061_6063del
NG_033079.1:g.3939_3941del
ENST00000700029.2:c.30_32del
ENST00000710265.1:c.30_32del
ENST00000472832.3:c.30_32del
ENST00000688922.2:c.30_32del
ENST00000700021.1:c.30_32del
ENST00000700022.1:c.30_32del
ENST00000706954.1:c.30_32del
ENST00000706955.1:c.30_32del
ENST00000686459.1:c.30_32del
ENST00000688158.1:c.30_32del
ENST00000688308.1:c.30_32del
ENST00000693560.1:c.549_551del
ENST00000371953.8:c.30_32del
ENST00000371953.7:c.30_32del
ENST00000462694.1:n.32_34del
ENST00000487939.1:n.51_53del
ENST00000610634.1:c.-73_-71del
NM_000314.5:c.30_32del
NM_000314.6:c.30_32del
NM_001304717.2:c.549_551del
NM_001304718.1:c.-676_-674del
NM_000314.7:c.30_32del
NM_001304717.5:c.549_551del
NM_001304718.2:c.-676_-674del
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Uncertain Significance

Met criteria codes 3
PM6 PM2_Supporting PS3_Moderate
Not Met criteria codes 1
PM4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
PTEN VCEP
PTEN c.30_32del (p.Ser10del) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.2.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). PM2_Supporting: Absent in large sequenced populations OR present at extremely low (<0.00001, 0.001%) allele frequency in the gnomAD cohort. (PMID 27535533). PS3_M: Functional studies supportive of a damaging effect on the gene or gene product. Score of this variant = -4.623 (≤ -1.11) on a high throughput phosphatase assay (PMID:29706350) PM6: Assumed de novo, but without confirmation of paternity and maternity in a patient with the disease and no family history. (internal laboratory contributor(s) SCV000580011.6)
Met criteria codes
PM6
Assumed de novo mutation in one individual with epilepsy, developmental delay with regression, and macrocephaly (SSCV000580011.6)
PM2_Supporting
Absent from gnomAD v2 and v4
PS3_Moderate
Mighell et al score of -4.628232038
Not Met criteria codes
PM4
Not in catalytic domain
Curation History
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