NM_000368.5:c.2194C>T

TSC1 · NP_000359.1:p.(His732Tyr) · NM_000368.5

GRCh37: chr9:135779052 G>A · GRCh38: chr9:132903665 G>A

Gene: TSC1 Transcript: NM_000368.5

Final call

Likely Benign

BS1 strong BP4 supporting benign BP6 supporting benign

Variant details

Gene

TSC1

Transcript

NM_000368.5

Protein

NP_000359.1:p.(His732Tyr)

gnomAD AF

0.0036008077319996824 (v4.1)

ClinVar

Benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_000368.5:c.2194C>T (p.His732Tyr) is a missense variant in TSC1, a gene in which loss-of-function variants cause tuberous sclerosis complex (autosomal dominant).

The variant is present in gnomAD v2.1 at an allele frequency of 0.387% (1093/282512 alleles) with 7 homozygotes, and in gnomAD v4.1 at 0.360% (5806/1612416 alleles) with 28 homozygotes. This frequency exceeds the 0.3% threshold for BS1 (strong benign).

The presence of 28 homozygous individuals in gnomAD v4.1 is incompatible with a highly penetrant autosomal dominant tumor suppressor disorder; homozygous loss of TSC1 function would be expected to cause severe disease.

Multiple in silico predictors support a benign interpretation: REVEL score 0.338 (below 0.5 pathogenic threshold), BayesDel score -0.064 (negative score), and SpliceAI max delta 0.09 (below 0.2 splicing threshold), meeting BP4 (supporting benign).

In ClinVar, 23 clinical laboratories classify this variant as Benign and 4 as Likely benign (Variation ID: 5103), meeting BP6 (supporting benign).

PMID:19918125 (Lugnier et al. 2009) characterized hamartin H732Y in vitro and demonstrated reduced tuberin binding (2.3-fold, p<0.05) and aberrant nuclear localization. However, the paper explicitly reported the allele at 0.5% frequency in the normal population and concluded it 'cannot be sufficient to cause TSC or FCD,' describing it as a low-penetrance predisposing variant at most.

Applying generic ACMG/AMP 2015 combination rules (PMID:25741868): one strong benign criterion (BS1) plus two supporting benign criteria (BP4, BP6) yields a final classification of Likely Benign.

Final determination: Generic ACMG/AMP 2015 fallback rules support a Likely Benign classification because either one strong benign criterion plus one supporting benign criterion, or at least two supporting benign criteria, are present.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_000368.5:c.2194C>T is a missense variant (p.His732Tyr); PVS1 is applicable only to null variants (nonsense, frameshift, canonical ±1,2 splice sites, initiation codon, single/multi-exon deletions). This variant does not fall into any null-variant bucket.	pvs1_generic_framework pvs1_variant_assessment
PS1	Not assessed	No known pathogenic variant resulting in the same amino acid change (His732Tyr) was identified. PS1 requires a previously classified pathogenic variant at the same residue with an identical predicted amino acid consequence.
PS2	Not met	One confirmed de novo occurrence reported (PMID:17304050) in a TSC proband with confirmed parental testing, but PS2 requires ≥2 de novo observations for strong evidence. A single de novo case is insufficient to meet PS2, especially given the variant is common in population databases (gnomAD AF 0.37%, 7–28 homozygotes).
PS3	Not met	PMID:19918125 (Lugnier et al. 2009) characterized hamartin H732Y in vitro: coimmunoprecipitation assays demonstrated 2.3-fold reduced tuberin binding (p<0.05, n=9 replicates), and the variant showed aberrant nuclear localization in HEK293T cells. However, the paper explicitly states this allele is present in 0.5% of the normal population and 'cannot be sufficient to cause TSC or FCD.' PS3 requires well-established functional studies showing a damaging effect in a disease-relevant context; the in vitro impairment is present but the variant's high population frequency and the authors' own conclusion that it is not disease-causing preclude application of PS3.	PMID:19918125
PS4	Not met	The variant has been observed in TSC patient cohorts (1/325 probands in PMID:17304050; also reported in PMID:15798777), but the prevalence in affected individuals does not significantly exceed the general population frequency of ~0.37% (gnomAD). No formal case-control study with a statistically significant odds ratio has been conducted.	gnomad_v2 gnomad_v4
PS5	Not assessed	No alternate pathogenic variant at the same nucleotide position (c.2194) has been identified and classified as pathogenic. PS5 requires a different nucleotide change at the same position with an established pathogenic classification.
PM1	Not met	Residue His732 lies outside the well-established TSC1 functional domains. The N-terminal TSC2-binding domain spans amino acids 1–266 and the C-terminal coiled-coil tuberin-binding domain spans amino acids 881–1084 (PMID:9580671). His732 is not in a critical functional domain, a recognized mutational hotspot, or a region where pathogenic missense variants are enriched.
PM2	Not met	The variant is present in gnomAD v2.1 at AF 0.00387 (0.387%, 1093/282512 alleles, 7 homozygotes) and in gnomAD v4.1 at AF 0.00360 (0.360%, 5806/1612416 alleles, 28 homozygotes). Both frequencies exceed the 0.1% threshold for PM2. The variant is common, not rare.	gnomad_v2 gnomad_v4
PM5	N/A	No same-residue comparator variants with a different pathogenic amino acid change could be confirmed by automated candidate harvesting. Classic PM5 semantics could not be established.	pm5_candidates
PM6	Not met	One presumed de novo occurrence without confirmation of paternity/maternity was reported (PMID:15798777). However, PM6 requires ≥2 independent assumed de novo events to reach moderate strength, and the variant's high population frequency (gnomAD AF 0.37%) makes a de novo interpretation unreliable. A single presumed de novo in the context of a common population variant does not meet PM6.	gnomad_v2 gnomad_v4
PP1	Not assessed	No published cosegregation data are available for this variant in families with multiple affected individuals. Cosegregation with disease in ≥3–4 affected family members would be needed to apply PP1.
PP2	N/A	PP2 applies to genes where missense variants are a common mechanism of disease and the gene has a low rate of benign missense variation (high missense Z-score). TSC1 has a missense Z-score that does not meet the threshold for PP2, and the variant is common in population databases.
PP3	Not met	Multiple in silico predictors suggest a benign impact: REVEL score 0.338 (threshold ≥0.5 for pathogenic), BayesDel score -0.064 (threshold >0 for pathogenic), SpliceAI max delta 0.09 (threshold ≥0.2 for splice effect). No computational evidence supports a deleterious effect.	revel bayesdel spliceai
PP4	Not assessed	PP4 requires detailed patient phenotype information and specificity scoring; insufficient phenotype data are available to assess whether the variant is enriched in patients with a phenotype highly specific for TSC1-related disease.
PP5	Not met	ClinVar classification for this variant is Benign (23 clinical laboratories) and Likely benign (4 laboratories); PP5 is applicable only when reputable sources classify the variant as pathogenic. The consensus benign classification precludes PP5.	clinvar
BA1	Not met	The overall gnomAD allele frequency is 0.37% (v2.1) and 0.36% (v4.1), which is below the 1% BA1 threshold. Although the Finnish subpopulation frequency reaches 1.38% (v2.1) with 3 homozygotes, the grpmax filtering allele frequency (upper bound of 95% CI for the highest subpopulation) is 0.62% (v2.1) and 0.38% (v4.1) — below 1%. Using the conservative grpmax FAF metric, BA1 is not met. However, BS1 is met (see below).	gnomad_v2 gnomad_v4
BS1	Met	The variant is present in gnomAD v2.1 at AF 0.387% (1093/282512 alleles, 7 homozygotes) and gnomAD v4.1 at AF 0.360% (5806/1612416 alleles, 28 homozygotes). Both overall frequencies exceed the 0.3% BS1 threshold. The presence of 7–28 apparently healthy homozygous individuals in population databases for an autosomal dominant tumor suppressor gene (TSC1) provides strong evidence that this variant is benign. PMID:19918125 independently reported the allele at 0.5% in the normal population and concluded it 'cannot be sufficient to cause TSC or FCD.'	gnomad_v2 gnomad_v4 PMID:19918125
BS2	Not assessed	BS2 (observed in a healthy adult individual for a fully penetrant disorder) is superseded by BS1, which provides stronger population-based evidence using allele frequency rather than individual observations.
BS3	Not met	No well-established functional studies demonstrate that the H732Y variant has no damaging effect on protein function. The available functional data (PMID:19918125) shows reduced tuberin binding and aberrant nuclear localization — a partially impaired phenotype, not a benign functional result. BS3 requires functional evidence showing no deleterious impact.	PMID:19918125
BS4	Not assessed	No published reports demonstrate lack of segregation of this variant with disease in affected families. The strong population evidence (BS1) provides comparable weight to BS4.
BP1	Not met	BP1 is applicable to missense variants in genes where primarily truncating variants cause disease. While TSC1 disease mechanism is loss-of-function, numerous pathogenic missense variants are also well-documented in TSC1. The gene does not have a predominantly truncating pathogenic variant spectrum, so BP1 does not apply.
BP2	N/A	BP2 applies to variants observed in trans with a pathogenic variant in a fully penetrant recessive disorder. TSC1-related tuberous sclerosis complex is an autosomal dominant condition; BP2 is not applicable.
BP3	N/A	Skipped: in-frame deletions/insertions in repetitive regions are not applicable to this missense substitution variant.
BP4	Met	Multiple in silico predictors consistently indicate a benign impact. REVEL score is 0.338 (below the 0.5 threshold for pathogenic prediction), BayesDel score is -0.064 (negative, favoring benign), and SpliceAI max delta is 0.09 (below the 0.2 threshold for splicing impact). All three orthogonal computational tools agree on a benign/non-damaging prediction.	revel bayesdel spliceai
BP5	Not assessed	BP5 requires an alternate molecular basis for disease in a case where the variant is observed. No such data were identified for this case; the strong population evidence (BS1) is the primary benign criterion.
BP6	Met	This variant is classified as Benign in ClinVar by 23 clinical laboratories and as Likely benign by 4 clinical laboratories (ClinVar Variation ID: 5103). The review status is 'criteria provided, single submitter.' The strong clinical consensus — 23 out of 27 classified submissions are 'Benign' — supports a benign interpretation under BP6.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants predicted not to affect splicing. c.2194C>T is a missense variant (p.His732Tyr), not a synonymous variant.

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