LHCGR p.Pro38=
c.114C>G · rs74469055 · VCV2159654
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.335%, 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 -0.71 | GERP -3 |
| Overall | ||
| CADD | 11.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.335%
African / African-American · 244/72,940 alleles
Filtering AF
0.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.287%
Overall
0.0171%
264/1,540,918 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.335% | 299 |
| Admixed American | 0.0157% | 6,357 |
| Remaining individualsnot grpmax-eligible | 0.0117% | 8,527 |
| South Asian | 0.00239% | 41,886 |
| European (non-Finnish) | 0.000262% | 381,688 |
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
- LHCGR
- Protein
- p.Pro38=
- Coding
- c.114C>G
- MANE Select
- NM_000233
- dbSNP
- rs74469055
- Type
- single nucleotide variant
- Location
- chr2:48755558 (GRCh38)
- Gene constraint
- LOEUF 1.056 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.95 · 4 PDB
- Residue 38
- the lrrnt domain
Similar variants
- LHCGR p.Arg124Ter Pathogenic/Likely pathogenic ★★ same type
- LHCGR p.Arg554Ter Pathogenic/Likely pathogenic ★★ same type
- LHCGR p.Asp564Gly Pathogenic ★★ ⚠ same type
- LHCGR p.Asp578Gly Pathogenic ★★ same type
- LHCGR p.Ile542Leu Pathogenic ★★ ⚠ same type
- LHCGR p.Thr577Ile Pathogenic/Likely pathogenic ★★ ⚠ same type
- LHCGR p.Ala344Asp Uncertain significance ★★ ⚠ same type
- LHCGR p.Arg695His 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/lhcgr-p-pro38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown