Is CHIT1 p.Ala366= (c.1098C>T) pathogenic?

CHIT1 p.Ala366= (c.1098C>T) is classified Likely benign in CHIT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-27). Very rare (popmax 0.00837%, sas); Associated with Chitotriosidase deficiency.

What condition is associated with CHIT1 p.Ala366= (c.1098C>T)?

CHIT1 p.Ala366= (c.1098C>T) is associated with Chitotriosidase deficiency (ClinVar).

How common is CHIT1 p.Ala366= (c.1098C>T) in the general population?

CHIT1 p.Ala366= (c.1098C>T) is very rare (popmax 0.00837%, sas) (gnomAD).

CHIT1 p.Ala366=

c.1098C>T · rs758032638 · VCV2053765

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00837%, sas)

Conditions

Chitotriosidase deficiency

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 -8.8	GERP -3.9
Overall
CADD	6.692	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00837% South Asian · 6/71,678 alleles

Filtering AF 0.0036% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00247%

Overall 0.00156% 21/1,346,720 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00837%	11,946
Admixed American	0.00388%	25,751
East Asian	0.00303%	33,032
African / African-American	0.0014%	71,648
European (non-Finnish)	0.00113%	88,531

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: CHIT1
Protein: p.Ala366=
Coding: c.1098C>T
MANE Select: NM_003465
dbSNP: rs758032638
Type: single nucleotide variant
Location: chr1:203217797 (GRCh38)
Gene constraint: LOEUF 1.147 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.72 · 23 PDB
Residue 366: a disulfide bond; the gh18 domain

Full CHIT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Chitotriosidase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHIT1 p.Ala366Asp Uncertain significance ★ ⚠ same residue
CHIT1 c.-13G>A Uncertain significance ★★ same condition
CHIT1 c.*119C>T Uncertain significance ★★ same condition
CHIT1 p.Arg128His Uncertain significance ★★ ⚠ same condition
CHIT1 p.Arg432Trp Uncertain significance ★★ ⚠ same condition
CHIT1 p.Pro451Arg Uncertain significance ★★ ⚠ same condition
CHIT1 c.25+8G>T Likely benign ★★ same condition
CHIT1 c.258-6T>C 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/chit1-p-ala366 (accessed [today's date]).

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