Is LRP2 p.Arg34Cys (c.100C>T) pathogenic?

LRP2 p.Arg34Cys (c.100C>T) is classified Uncertain significance in LRP2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-22). AlphaMissense: ambiguous (0.4088); Very rare (popmax 0.00195%, nfe); Associated with Donnai-Barrow syndrome.

What condition is associated with LRP2 p.Arg34Cys (c.100C>T)?

LRP2 p.Arg34Cys (c.100C>T) is associated with Donnai-Barrow syndrome (ClinVar).

How common is LRP2 p.Arg34Cys (c.100C>T) in the general population?

LRP2 p.Arg34Cys (c.100C>T) is very rare (popmax 0.00195%, nfe) (gnomAD).

What do computational predictors say about LRP2 p.Arg34Cys (c.100C>T)?

AlphaMissense predicts ambiguous (score 0.4088) — an in-silico prediction, not a clinical call.

LRP2 p.Arg34Cys

c.100C>T · rs747942310 · VCV1377545

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.4088 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00195%, nfe)

Conditions

Donnai-Barrow syndrome

Computational evidence

Protein change
AlphaMissense	0.4088	ambiguous
REVEL	0.732	pathogenic-leaning
SaProt	—	not scored · why
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.5	GERP 2, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 156 kb · p 7.9e-06 · regional, not allelic
Overall
CADD	25.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00195% European (non-Finnish) · 23/1,179,582 alleles

Filtering AF 0.0013% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00108%

Overall 0.00161% 26/1,613,484 alleles · very rare exomes 22/1,461,366 · genomes 4/152,118 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00195%	51,286
Admixed American	0.00167%	59,984
Remaining individualsnot grpmax-eligible	0.0016%	62,460
South Asian	0.0011%	91,074

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: LRP2
Protein: p.Arg34Cys
Coding: c.100C>T
MANE Select: NM_004525
dbSNP: rs747942310
Type: single nucleotide variant
Location: chr2:169320864 (GRCh38)
Gene constraint: LOEUF 0.352 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 34: the ldl-receptor class a 1 domain

Full LRP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Donnai-Barrow syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LRP2 p.Arg34His Uncertain significance ★★ same residue
LRP2 c.12019+1G>A Likely pathogenic ★★ same condition
LRP2 c.2639+1G>A Pathogenic/Likely pathogenic ★★ same condition
LRP2 c.3667+1G>A Pathogenic/Likely pathogenic ★★ same condition
LRP2 c.8452+1G>A Pathogenic ★★ same condition
LRP2 p.Arg1953Ter Pathogenic/Likely pathogenic ★★ same condition
LRP2 p.Arg2225Ter Pathogenic/Likely pathogenic ★★ same condition
LRP2 p.Arg278Ter Pathogenic/Likely pathogenic ★★ 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/lrp2-p-arg34cys (accessed [today's date]).

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