Is CHST6 p.Arg5= (c.15C>G) pathogenic?

CHST6 p.Arg5= (c.15C>G) is classified Likely benign in CHST6 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-23). Ultra-rare (popmax 0.0193%, amr); Associated with macular corneal dystrophy.

What condition is associated with CHST6 p.Arg5= (c.15C>G)?

CHST6 p.Arg5= (c.15C>G) is associated with macular corneal dystrophy (ClinVar).

How common is CHST6 p.Arg5= (c.15C>G) in the general population?

CHST6 p.Arg5= (c.15C>G) is ultra-rare (popmax 0.0193%, amr) (gnomAD).

How is Macular corneal dystrophy inherited?

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

CHST6 p.Arg5=

c.15C>G · VCV4739778

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0193%, amr)

Conditions

macular 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 -0.72	GERP -3.1
Overall
CADD	0.311	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0193% Admixed American · 10/51,818 alleles

Filtering AF 0.0104% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00788%

Overall 0.00078% 11/1,409,534 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0193%	5,182
Remaining individualsnot grpmax-eligible	0.00165%	60,676

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: CHST6
Protein: p.Arg5=
Coding: c.15C>G
MANE Select: NM_021615
Type: single nucleotide variant
Location: chr16:75479814 (GRCh38)
Gene constraint: LOEUF 1.71 · pLI 0.26 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 90.66

Full CHST6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

macular corneal dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Macular corneal dystrophy (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-9 / 100 000 (United States)

Similar variants

CHST6 p.Arg5Pro Uncertain significance ★ ⚠ same residue
CHST6 p.Arg5Cys Uncertain significance ★ ⚠ same residue
CHST6 p.Arg5His Uncertain significance ★ ⚠ same residue
CHST6 p.Ala128Thr Likely pathogenic ★★ ⚠ same condition
CHST6 p.Arg127Cys Pathogenic ★★ same condition
CHST6 p.Arg140Ter Pathogenic ★★ same condition
CHST6 p.Arg211Gln Pathogenic ★★ ⚠ same condition
CHST6 p.Cys102Gly 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/chst6-p-arg5 (accessed [today's date]).

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