LCT p.Arg1002=
c.3006G>A · rs114815229 · VCV331191
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.73%, afr)
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 -0.98 | GERP -1.3 |
| Overall | ||
| CADD | 2.945 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.73%
African / African-American · 1,300/75,034 alleles
Filtering AF
1.65%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.62%
Overall
0.0943%
1,522/1,614,194 alleles · low-frequency
exomes 741/1,461,884 · genomes 781/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.73% | 58 |
| Admixed American | 0.167% | 600 |
| Remaining individualsnot grpmax-eligible | 0.142% | 702 |
| Middle Eastern | 0.0495% | 2,021 |
| South Asian | 0.00988% | 10,121 |
| European (non-Finnish) | 0.00178% | 56,193 |
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
- LCT
- Protein
- p.Arg1002=
- Coding
- c.3006G>A
- MANE Select
- NM_002299
- dbSNP
- rs114815229
- Type
- single nucleotide variant
- Location
- chr2:135809341 (GRCh38)
- Gene constraint
- LOEUF 0.62 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.63
- Residue 1002
- the 'glycosyl hydrolase-1 3; region iii. phlorizin hydrolase/glycosylceramidase activity' region
Similar variants
- LCT c.4866+2T>G Likely pathogenic ★★ same type
- LCT p.Gln1179Ter Pathogenic/Likely pathogenic ★★ same type
- LCT p.Lys787Ter Pathogenic/Likely pathogenic ★★ same type
- LCT p.Tyr1390Ter Pathogenic ★★ same type
- LCT c.4173+5G>A Uncertain significance ★★ same type
- LCT p.Ala1398Glu Uncertain significance ★★ ⚠ same type
- LCT p.Ala1483Thr Uncertain significance ★★ ⚠ same type
- LCT p.Ala148Gly Uncertain significance ★★ ⚠ 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/lct-p-arg1002 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown