Variant detail

KCNH2Y652X

c.1955X · residue 652 · Y → X
Technical Plain language
HGVS annotation

ClinVar-style identity and transcript context

ClinVar-style HGVS
NM_000238.4(KCNH2):c.1955X (Y652X)
HGVSc
c.1955X
cDNA change
c.1955X
RefSeq transcript
NM_000238.4
Ensembl transcript
ENST00000262186.10
Protein HGVS
Y652X
Genomic coordinate
Chr7 150648199
ClinVar annotation
Not annotated in local ClinVar field
LQT2 penetrance Low risk
0% CI pending
0%20%50%100%

Emerging evidence · n=6 6 observed LQT2 carriers · NA hypothetical affected and NA hypothetical unaffected

One-sentence summary

Roughly fewer than 1 in 100 people who carry Y652X are estimated to eventually be diagnosed with Long QT type 2 — low risk penetrance, based on 6 carriers reported so far.

Structure: Not annotated. Functional evidence: MAVE 0% WT.

Executive summary

Sources used for interpretation

The LQT2 penetrance estimate combines observed carrier counts with a feature-based model starting point. Other rows summarize supporting annotations for interpretation; not every row is a direct input to the model.

Estimatemodel output Observedmeasured in people/assays Model inputassumed, not observed Predictedcomputational Externalthird-party
EstimateModel-based penetrance estimate0% · Low risk
Model inputHypothetical observationsNA affected · NA unaffected
ObservedObserved carriers (literature + cohorts)6 · Emerging evidence
ObservedPopulation observations (gnomAD v4)0 alleles
PredictedIn silico predictorsREVEL · PolyPhen-2 · PROVEAN · BLAST-PSSM
ObservedFunctional / MAVE dataSevere trafficking loss · 0 studies
PredictedStructural contextNot annotated
ExternalAutomated ACMG reviewNot a classification
ExternalExternal databasesClinVar · gnomAD · UniProt

Evidence

Carriers observed
6
6 LQT2 · 0 unaffected · 0 gnomAD
Model prior: NA hypothetical affected · NA hypothetical unaffected
Emerging evidence
Functional data
Severe trafficking loss
MAVE 0% WT · 0 published functional studies
Predictors and density
REVEL—range 0-1
LQT2 density—range 0-1
PolyPhen-2—range 0-1
PROVEAN—cutoff <= -2.5
BLAST-PSSM—lower = less tolerated
Overall0/5
Range labels show the expected scale or cutoff. Calls are rough orientation from published cutoffs (hover a row) — not a clinical classification.

Automated ACMG/AMP review prompts

Generated from available data — not a clinical classification
PS3met · strong/moderate
Functional studies or MAVE support effect
PM1not met
Hotspot or high LQT2 density
PM2met · moderate
Absent or extremely rare in population data
PP3not met
Computational predictors support effect
BS1not met
Allele frequency too high for disorder

Reported carrier data

Paper / cohort Carriers LQT2 / affected Unaffected / ambiguous Other observations Variant context
Year 2009 · clinical carrier record
6 6 LQT2 0 unaffected / ambiguous Not separately annotated
Variant Y652X
Curated carrier-count row
gnomAD population observations (v4) 0 0 LQT2 0 Population observations; not known affected cases. gnomAD v4 allele count.
Combined literature, cohort, and gnomAD 6 6 LQT2 0 Combined totals used in the penetrance estimate. Curated carrier totals for this variant.
Hypothetical observations from model prior (not observed patients) NA NA hypothetical LQT2 affected NA hypothetical unaffected Feature-based pseudo-counts added before observed carriers. Model input; not literature or gnomAD evidence.

Model starting point. The penetrance model starts with NA hypothetical affected and NA hypothetical unaffected observations derived from variant features, then updates that starting point with the real carrier counts above. As observed carrier counts grow, this feature-based starting point has less influence.

External resources
ClinVar Open gnomAD Open UniProt