LIPH p.Cys53=
c.159C>T · rs61741645 · VCV2063738
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.363%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -10 | GERP -3.7 |
| Overall | ||
| CADD | 0.228 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.363%
African / African-American · 272/74,990 alleles
Filtering AF
0.327%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.314%
Overall
0.0227%
367/1,613,652 alleles · rare
exomes 235/1,461,360 · genomes 132/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.363% | 276 |
| Middle Eastern | 0.116% | 866 |
| Remaining individualsnot grpmax-eligible | 0.0384% | 2,604 |
| East Asian | 0.0178% | 5,610 |
| Admixed American | 0.0167% | 5,995 |
| European (non-Finnish) | 0.00364% | 27,436 |
| South Asian | 0.0033% | 30,342 |
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
- LIPH
- Protein
- p.Cys53=
- Coding
- c.159C>T
- MANE Select
- NM_139248
- dbSNP
- rs61741645
- Type
- single nucleotide variant
- Location
- chr3:185535023 (GRCh38)
- Gene constraint
- LOEUF 0.811 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.89
Similar variants
- LIPH p.Arg110Ter Pathogenic/Likely pathogenic ★★ same type
- LIPH p.Cys246Ser Pathogenic/Likely pathogenic ★★ same type
- LIPH p.His248Asn Pathogenic/Likely pathogenic ★★ same type
- LIPH p.Ala180Gly Uncertain significance ★★ ⚠ same type
- LIPH p.Arg110Leu Uncertain significance ★★ ⚠ same type
- LIPH p.Ile336Met Uncertain significance ★★ ⚠ same type
- LIPH p.Thr286Met Uncertain significance ★★ ⚠ same type
- LIPH c.1094+29C>T 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/liph-p-cys53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown