Is CHIT1 p.Ala123= (c.369C>T) pathogenic?

CHIT1 p.Ala123= (c.369C>T) is classified Likely benign in CHIT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-12). Ultra-rare (popmax 0.0533%, afr); Associated with Chitotriosidase deficiency.

What condition is associated with CHIT1 p.Ala123= (c.369C>T)?

CHIT1 p.Ala123= (c.369C>T) is associated with Chitotriosidase deficiency (ClinVar).

How common is CHIT1 p.Ala123= (c.369C>T) in the general population?

CHIT1 p.Ala123= (c.369C>T) is ultra-rare (popmax 0.0533%, afr) (gnomAD).

CHIT1 p.Ala123=

c.369C>T · rs188371763 · VCV1564214

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0533%, afr)

Conditions

Chitotriosidase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.24 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.9	GERP -1.4, phastCons 0.016
Overall
CADD	6.858	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0533% African / African-American · 40/75,058 alleles

Filtering AF 0.0401% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0356%

Overall 0.00279% 45/1,614,232 alleles · ultra-rare exomes 17/1,461,888 · genomes 28/152,344 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0533%	1,876
Remaining individualsnot grpmax-eligible	0.0064%	15,626
Admixed American	0.00167%	60,038

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.Ala123=
Coding: c.369C>T
MANE Select: NM_003465
dbSNP: rs188371763
Type: single nucleotide variant
Location: chr1:203223606 (GRCh38)
Gene constraint: LOEUF 1.147 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.72 · 23 PDB
Residue 123: the gh18 domain; an α-helix

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 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
CHIT1 p.Ala442Gly 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-ala123 (accessed [today's date]).

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