Is LRP5 p.Val600= (c.1800C>T) pathogenic?

LRP5 p.Val600= (c.1800C>T) is classified Benign/Likely benign in LRP5 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-26). Rare (popmax 0.27%, eas); Associated with Inborn genetic diseases.

What condition is associated with LRP5 p.Val600= (c.1800C>T)?

LRP5 p.Val600= (c.1800C>T) is associated with Inborn genetic diseases (ClinVar).

How common is LRP5 p.Val600= (c.1800C>T) in the general population?

LRP5 p.Val600= (c.1800C>T) is rare (popmax 0.27%, eas) (gnomAD).

LRP5 p.Val600=

c.1800C>T · rs200800275 · VCV797083

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.27%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -14	GERP -3.9
Overall
CADD	0.645	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.27% East Asian · 121/44,868 alleles

Filtering AF 0.231% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.216%

Overall 0.00911% 147/1,613,190 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.27%	371
Remaining individualsnot grpmax-eligible	0.0128%	7,805
Admixed American	0.00667%	15,002
South Asian	0.0033%	30,343
African / African-American	0.00267%	37,512
European (non-Finnish)	0.000763%	131,111

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: LRP5
Protein: p.Val600=
Coding: c.1800C>T
MANE Select: NM_002335
dbSNP: rs200800275
Type: single nucleotide variant
Location: chr11:68403698 (GRCh38)
Gene constraint: LOEUF 0.482 · pLI 0.94 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 78.65
Residue 600: the 'beta-propeller 2' region

Full LRP5 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

LRP5 p.Val600Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
LRP5 p.Arg1078Ter Pathogenic ★★ same condition
LRP5 p.Arg570Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
LRP5 p.Ala1214Val Uncertain significance ★★ ⚠ same condition
LRP5 p.Ala1265Pro Uncertain significance ★★ ⚠ same condition
LRP5 p.Ala1306Thr Uncertain significance ★★ ⚠ same condition
LRP5 p.Ala1491Pro Uncertain significance ★★ ⚠ same condition
LRP5 p.Ala179Val 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/lrp5-p-val600 (accessed [today's date]).

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