Is CHIT1 p.Ala170= (c.510C>G) pathogenic?

CHIT1 p.Ala170= (c.510C>G) is classified Likely benign in CHIT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-25). Absent from gnomAD v4.1; Associated with Chitotriosidase deficiency.

What condition is associated with CHIT1 p.Ala170= (c.510C>G)?

CHIT1 p.Ala170= (c.510C>G) is associated with Chitotriosidase deficiency (ClinVar).

How common is CHIT1 p.Ala170= (c.510C>G) in the general population?

CHIT1 p.Ala170= (c.510C>G) is absent from gnomAD v4.1 (gnomAD).

CHIT1 p.Ala170=

c.510C>G · rs2526371522 · VCV2848639

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 0.59	GERP -1.9, phastCons 0.12
Overall
CADD	8.108	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CHIT1
Protein: p.Ala170=
Coding: c.510C>G
MANE Select: NM_003465
dbSNP: rs2526371522
Type: single nucleotide variant
Location: chr1:203223230 (GRCh38)
Gene constraint: LOEUF 1.147 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.72 · 23 PDB
Residue 170: 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 p.Ala170Ser Conflicting classifications of pathogenicity ★ ⚠ 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-ala170 (accessed [today's date]).

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