Is LIPH p.Asp17= (c.51C>T) pathogenic?

LIPH p.Asp17= (c.51C>T) is classified Benign in LIPH (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-02). Rare (popmax 0.74%, eas).

How common is LIPH p.Asp17= (c.51C>T) in the general population?

LIPH p.Asp17= (c.51C>T) is rare (popmax 0.74%, eas) (gnomAD).

LIPH p.Asp17=

c.51C>T · rs139264479 · VCV2056690

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.74%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.20	acceptor gain, 1 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP -0.27	GERP -3.2
Overall
CADD	8.742	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.74% East Asian · 332/44,882 alleles

Filtering AF 0.674% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.649%

Overall 0.165% 2,660/1,613,882 alleles · rare exomes 2,225/1,461,658 · genomes 435/152,224 · joint denominator

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	2.65%	38
East Asiangrpmax	0.74%	135
Remaining individualsnot grpmax-eligible	0.163%	613
Admixed American	0.147%	682
South Asian	0.119%	843
Ashkenazi Jewishnot grpmax-eligible	0.098%	1,021
Middle Eastern	0.066%	1,516
European (non-Finnish)	0.0253%	3,960
African / African-American	0.00933%	10,715

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Asp17=
Coding: c.51C>T
MANE Select: NM_139248
dbSNP: rs139264479
Type: single nucleotide variant
Location: chr3:185535131 (GRCh38)
Gene constraint: LOEUF 0.811 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.89

Full LIPH gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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-asp17 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown