Is TSC2 p.Asp1644= (c.4932C>T) pathogenic?

TSC2 p.Asp1644= (c.4932C>T) is classified Likely benign in TSC2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-10-05). Very rare (popmax 6.21e-05%); Associated with hereditary neoplastic syndrome.

What condition is associated with TSC2 p.Asp1644= (c.4932C>T)?

TSC2 p.Asp1644= (c.4932C>T) is associated with hereditary neoplastic syndrome, tuberous sclerosis 2 (ClinVar).

How common is TSC2 p.Asp1644= (c.4932C>T) in the general population?

TSC2 p.Asp1644= (c.4932C>T) is very rare (popmax 6.21e-05%) (gnomAD).

TSC2 p.Asp1644=

c.4932C>T · rs1395198412 · VCV1533030

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 6.21e-05%)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.003	GERP -3.8, phastCons 0.76
Overall
CADD	0.754	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.21e-05%

Overall 6.21e-05% 1/1,610,442 alleles · very rare exomes 1/1,458,080 · genomes 0/152,362 · joint denominator

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.Asp1644=
Coding: c.4932C>T
MANE Select: NM_000548
dbSNP: rs1395198412
Type: single nucleotide variant
Location: chr16:2086814 (GRCh38)
Gene constraint: LOEUF 0.203 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 68.81 · 2 PDB
Residue 1644: the rap-gap domain; a β-strand

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 2

Similar variants

TSC2 p.Asp1644Asn Likely benign ★★ ⚠ same residue
TSC2 p.Asp1644Tyr Pathogenic ★ same residue
TSC2 p.Asp1644Glu Uncertain significance ★ ⚠ 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

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-asp1644 (accessed [today's date]).

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