Is TACSTD2 c.*48G>A pathogenic?

TACSTD2 c.48G>A is classified Benign in TACSTD2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-01-12). Common (popmax 12.8%, mid) — too common for a highly-penetrant pathogenic allele; Associated with gelatinous drop-like corneal dystrophy.

What condition is associated with TACSTD2 c.*48G>A?

TACSTD2 c.*48G>A is associated with gelatinous drop-like corneal dystrophy (ClinVar).

How is Gelatinous drop-like corneal dystrophy inherited?

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

TACSTD2 c.*48G>A

Q: How common is TACSTD2 c.*48G>A in the general population?

TACSTD2 c.*48G>A is common (popmax 12.8%, mid) — too common for a highly-penetrant pathogenic allele (gnomAD).

rs41311174 · VCV297763

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Common

common (popmax 12.8%, mid) — too common for a highly-penetrant pathogenic allele

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 -3.3	GERP -3.6
Overall
CADD	4.036	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 12.8% Middle Eastern · 772/6,014 alleles

Filtering AF 12.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 11.8%

Overall 8.79% 140,377/1,596,804 alleles · common exomes 128,589/1,444,510 · genomes 11,788/152,294 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	12.8%	8
Amishnot grpmax-eligible	12.4%	8
Ashkenazi Jewishnot grpmax-eligible	9.97%	10
European (non-Finnish)	9.67%	10
Remaining individualsnot grpmax-eligible	8.88%	11
Finnishnot grpmax-eligible	7.78%	13
South Asian	6.29%	16
Admixed American	5.84%	17
African / African-American	5.3%	19
East Asian	0.11%	913

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
Coding: c.*48G>A
MANE Select: NM_002353
dbSNP: rs41311174
Type: single nucleotide variant
Location: chr1:58576137 (GRCh38)
Gene constraint: LOEUF 1.868 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.11 · 7 PDB

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-c-star-48g-a (accessed [today's date]).

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