Is TACSTD2 p.Glu254= (c.762G>A) pathogenic?

TACSTD2 p.Glu254= (c.762G>A) is classified Benign/Likely benign in TACSTD2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-14). Rare (popmax 0.28%, afr); Associated with gelatinous drop-like corneal dystrophy.

What condition is associated with TACSTD2 p.Glu254= (c.762G>A)?

TACSTD2 p.Glu254= (c.762G>A) is associated with gelatinous drop-like corneal dystrophy (ClinVar).

How common is TACSTD2 p.Glu254= (c.762G>A) in the general population?

TACSTD2 p.Glu254= (c.762G>A) is rare (popmax 0.28%, afr) (gnomAD).

How is Gelatinous drop-like corneal dystrophy inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

TACSTD2 p.Glu254=

c.762G>A · rs144787622 · VCV297767

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.28%, afr)

Conditions

gelatinous drop-like corneal dystrophy

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 1.3	GERP -3.7, phastCons 1
Overall
CADD	13.01	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.28% African / African-American · 210/75,018 alleles

Filtering AF 0.249% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.237%

Overall 0.0141% 228/1,613,444 alleles · rare exomes 114/1,461,178 · genomes 114/152,266 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.28%	357
Admixed American	0.0234%	4,282
Remaining individualsnot grpmax-eligible	0.00641%	15,613

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: TACSTD2
Protein: p.Glu254=
Coding: c.762G>A
MANE Select: NM_002353
dbSNP: rs144787622
Type: single nucleotide variant
Location: chr1:58576395 (GRCh38)
Gene constraint: LOEUF 1.868 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.11 · 7 PDB
Residue 254: a β-strand

Full TACSTD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

gelatinous drop-like corneal dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Gelatinous drop-like corneal dystrophy (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood
Prevalence: 1-9 / 1 000 000 (Japan)

Similar variants

TACSTD2 c.-56C>G Uncertain significance ★★ same condition
TACSTD2 p.Gly276Asp Uncertain significance ★★ ⚠ same condition
TACSTD2 p.Gly59Ser Uncertain significance ★★ ⚠ same condition
TACSTD2 c.-169G>A Benign ★★ same condition
TACSTD2 c.-54A>C Benign ★★ same condition
TACSTD2 c.*202A>G Benign ★★ same condition
TACSTD2 c.*280T>C Benign ★★ same condition
TACSTD2 c.*396T>C Likely benign ★★ 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/tacstd2-p-glu254 (accessed [today's date]).

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