LIPH p.Asn341=
c.1023T>C · rs142603972 · VCV2919509
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0418%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.073 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.53 | GERP -3.5 |
| Overall | ||
| CADD | 0.973 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0418%
African / African-American · 31/74,216 alleles
Filtering AF
0.0302%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0263%
Overall
0.00287%
45/1,569,650 alleles · ultra-rare
exomes 26/1,417,370 · genomes 19/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0418% | 2,394 |
| East Asian | 0.0112% | 8,936 |
| Admixed American | 0.00834% | 11,989 |
| Remaining individualsnot grpmax-eligible | 0.00656% | 15,252 |
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.Asn341=
- Coding
- c.1023T>C
- MANE Select
- NM_139248
- dbSNP
- rs142603972
- Type
- single nucleotide variant
- Location
- chr3:185514481 (GRCh38)
- Gene constraint
- LOEUF 0.811 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.89
- Residue 341
- a UniProt-annotated variant site (in arwh2)
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-asn341 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown