Is TSC2 p.Ala415Val (c.1244C>T) pathogenic?

TSC2 p.Ala415Val (c.1244C>T) is classified Conflicting classifications of pathogenicity in TSC2 (ClinVar, Conflicting submitters, 16 submitters; last evaluated 2026-01-26). AlphaMissense: likely benign (0.1746); Ultra-rare (popmax 0.0304%, nfe); Associated with hereditary neoplastic syndrome.

What condition is associated with TSC2 p.Ala415Val (c.1244C>T)?

TSC2 p.Ala415Val (c.1244C>T) is associated with hereditary neoplastic syndrome, tuberous sclerosis, tuberous sclerosis 2 (ClinVar).

How common is TSC2 p.Ala415Val (c.1244C>T) in the general population?

TSC2 p.Ala415Val (c.1244C>T) is ultra-rare (popmax 0.0304%, nfe) (gnomAD).

What do computational predictors say about TSC2 p.Ala415Val (c.1244C>T)?

AlphaMissense predicts likely benign (score 0.1746) — an in-silico prediction, not a clinical call.

TSC2 p.Ala415Val

c.1244C>T · rs374936223 · VCV184138

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 16 submitters

AlphaMissense

likely benign

0.1746 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0304%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.1746	likely benign
REVEL	0.56	indeterminate
SaProt	LLR -7.87	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	Δ0.33	donor loss, 4 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 7.6	GERP 1.8, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 37 kb · p 0.88 · regional, not allelic
Overall
CADD	24.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0304% European (non-Finnish) · 359/1,180,014 alleles

Filtering AF 0.0278% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0267%

Overall 0.0237% 383/1,613,972 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0304%	3,287
Finnishnot grpmax-eligible	0.0109%	9,139
Remaining individualsnot grpmax-eligible	0.0096%	10,414
African / African-American	0.00934%	10,702
East Asian	0.00223%	44,896
South Asian	0.0022%	45,544
Admixed American	0.00167%	60,008

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: TSC2
Protein: p.Ala415Val
Coding: c.1244C>T
MANE Select: NM_000548
dbSNP: rs374936223
Type: single nucleotide variant
Location: chr16:2061995 (GRCh38)
Gene constraint: LOEUF 0.203 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 68.81 · 2 PDB
Residue 415: an α-helix

Full TSC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: tuberous sclerosis tuberous sclerosis 2

Similar variants

TSC2 p.Ala415Glu Uncertain significance ★ ⚠ same residue
TSC2 p.Ala415= Likely benign ★ same residue
TSC2 c.1257+1G>A Pathogenic ★★ same condition
TSC2 c.1258-2A>G Pathogenic ★★ same condition
TSC2 c.1361+1G>A Pathogenic/Likely pathogenic ★★ same condition
TSC2 c.1361+1G>T Pathogenic/Likely pathogenic ★★ same condition
TSC2 c.1362-1G>A Pathogenic ★★ same condition
TSC2 c.138+2T>C Pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/tsc2-p-ala415val (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown