Is LIPH p.Arg412Gln (c.1235G>A) pathogenic?

LIPH p.Arg412Gln (c.1235G>A) is classified Uncertain significance in LIPH (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-26). AlphaMissense: likely benign (0.0763); Very rare (popmax 0.00549%, sas); Associated with Inborn genetic diseases.

What condition is associated with LIPH p.Arg412Gln (c.1235G>A)?

LIPH p.Arg412Gln (c.1235G>A) is associated with Inborn genetic diseases (ClinVar).

How common is LIPH p.Arg412Gln (c.1235G>A) in the general population?

LIPH p.Arg412Gln (c.1235G>A) is very rare (popmax 0.00549%, sas) (gnomAD).

What do computational predictors say about LIPH p.Arg412Gln (c.1235G>A)?

AlphaMissense predicts likely benign (score 0.0763) — an in-silico prediction, not a clinical call.

LIPH p.Arg412Gln

c.1235G>A · VCV4047513

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0763 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00549%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0763	likely benign
REVEL	0.143	moderately benign-leaning
SaProt	LLR -6.26	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.23	acceptor loss, 39 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 3.3	GERP 0.61, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 44 kb · p 0.056 · regional, not allelic
Overall
CADD	20.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00549% South Asian · 5/91,082 alleles

Filtering AF 0.0021% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00164%

Overall 0.0026% 42/1,613,988 alleles · very rare exomes 38/1,461,876 · genomes 4/152,112 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00549%	18,216
East Asian	0.00445%	22,447
Admixed American	0.00333%	29,992
Remaining individualsnot grpmax-eligible	0.0032%	31,245
European (non-Finnish)	0.00263%	38,065

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.Arg412Gln
Coding: c.1235G>A
MANE Select: NM_139248
Type: single nucleotide variant
Location: chr3:185511557 (GRCh38)
Gene constraint: LOEUF 0.811 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.89
Residue 412: a UniProt-annotated variant site (in arwh2)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LIPH p.Ala180Gly Uncertain significance ★★ ⚠ same condition
LIPH p.Arg110Leu Uncertain significance ★★ ⚠ same condition
LIPH p.Ile336Met Uncertain significance ★★ ⚠ same condition
LIPH p.Ala180Thr Uncertain significance ★ ⚠ same condition
LIPH p.Ala198Val Uncertain significance ★ ⚠ same condition
LIPH p.Ala267Glu Uncertain significance ★ ⚠ same condition
LIPH p.Ala54Thr Uncertain significance ★ ⚠ same condition
LIPH p.Arg110Gln Uncertain significance ★ ⚠ same condition

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-arg412gln (accessed [today's date]).

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