CHIT1 p.Phe58=
c.174C>T · rs963060367 · VCV777104
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00333%, amr)
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 -1.3 | GERP -3.9 |
| Overall | ||
| CADD | 2.119 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00333%
Admixed American · 2/60,012 alleles
Filtering AF
0.000553%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000207%
Overall
0.000496%
8/1,614,104 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00333% | 30,006 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| African / African-American | 0.00133% | 74,936 |
| South Asian | 0.0011% | 91,086 |
| European (non-Finnish) | 0.000169% | 590,023 |
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.Phe58=
- Coding
- c.174C>T
- MANE Select
- NM_003465
- dbSNP
- rs963060367
- Type
- single nucleotide variant
- Location
- chr1:203225752 (GRCh38)
- Gene constraint
- LOEUF 1.147 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.72 · 23 PDB
- Residue 58
- the gh18 domain; a β-strand
Similar variants
- CHIT1 c.-13G>A Uncertain significance ★★ same type
- CHIT1 c.*119C>T Uncertain significance ★★ same type
- CHIT1 p.Arg128His Uncertain significance ★★ ⚠ same type
- CHIT1 p.Arg432Trp Uncertain significance ★★ ⚠ same type
- CHIT1 p.Pro451Arg Uncertain significance ★★ ⚠ same type
- CHIT1 c.25+8G>T Likely benign ★★ same type
- CHIT1 c.258-6T>C Benign ★★ same type
- CHIT1 p.Ala442Gly Benign ★★ same type
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-phe58 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown