Is CHST6 p.Cys165Ser (c.494_495delinsCT) pathogenic?

CHST6 p.Cys165Ser (c.494495delinsCT) is classified Conflicting classifications of pathogenicity in CHST6 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2022-04-06). Absent from gnomAD; Associated with macular corneal dystrophy.

What condition is associated with CHST6 p.Cys165Ser (c.494_495delinsCT)?

CHST6 p.Cys165Ser (c.494_495delinsCT) is associated with macular corneal dystrophy (ClinVar).

How common is CHST6 p.Cys165Ser (c.494_495delinsCT) in the general population?

CHST6 p.Cys165Ser (c.494_495delinsCT) is absent from gnomAD (gnomAD).

How is Macular corneal dystrophy inherited?

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

CHST6 p.Cys165Ser

c.494_495delinsCT · rs2080109094 · VCV1029816

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 · substitutions only
Constraint at this position
Conservation	phyloP 4.6	GERP 1, phastCons 1
Regional constraint	o/e 1.19	unconstrained · MANE · 1,184 bp · p 3.9e-06 · regional, not allelic

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CHST6
Protein: p.Cys165Ser
Coding: c.494_495delinsCT
MANE Select: NM_021615
dbSNP: rs2080109094
Type: Indel
Location: chr16:75479334 (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.Cys165Ter Likely pathogenic ★ same residue
CHST6 p.Glu283Ter Pathogenic/Likely pathogenic ★★ same condition
CHST6 p.Trp2_Leu3delinsTer Pathogenic ★ same condition
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-cys165ser (accessed [today's date]).

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