# NM_004525.3(LRP2):c.639C>T (p.Asp213=)

https://sugi.bio/variant/lrp2-p-asp213

## Summary

**LRP2 p.Asp213= (c.639C>T)** is classified **Benign/Likely benign** in LRP2 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-02-04). Common (popmax 51.4%, amr) — too common for a highly-penetrant pathogenic allele; Associated with Donnai-Barrow syndrome.

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs2229266 · 9 submitters · 1 linked condition · common (popmax 51.4%, amr) — too common for a highly-penetrant pathogenic allele

## For patients & families {#patients}

This is a change in the LRP2 gene that is classified as benign/likely benign — not considered disease-causing, submitted by 9 submitters, and is linked to Donnai-Barrow syndrome.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Clinical trials | 1 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0001899/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [LRP2](https://sugi.bio/atlas/gene/LRP2/) |
| Protein change (HGVS p.) | p.Asp213= |
| Coding change (HGVS c.) | c.639C>T |
| MANE Select transcript | [NM_004525](https://www.ncbi.nlm.nih.gov/nuccore/NM_004525) |
| dbSNP | [rs2229266](https://www.ncbi.nlm.nih.gov/snp/rs2229266/) |
| Variant type | single nucleotide variant |
| Location | chr2:169294161-169294161 (GRCh38) |
| ClinVar | [VCV129533](https://www.ncbi.nlm.nih.gov/clinvar/variation/129533/) |

**All HGVS expressions:** `LRG_1300:g.73452C>T`, `LRG_1300t1:c.639C>T`, `NC_000002.11:g.170150671G>A`, `NC_000002.12:g.169294161G>A`, `NG_012634.1:g.73452C>T`, `NM_004525.3:c.639C>T`

## Computational & population evidence {#evidence}

**Concordance:** Evidence sources **disagree** — common (popmax 51.4%, amr) — too common for a highly-penetrant pathogenic allele.

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 0.768, GERP -2.23, phastCons 0.952 — weakly conserved position
- CADD: **PHRED 10.57**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **51.4%** (amr) · FAF95 50.9% · FAF99 50.7% · 30,808/59,948 in the highest group · 448,907/1,602,868 alleles overall — common (popmax 51.4%, amr) — too common for a highly-penetrant pathogenic allele.

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 51.4% | 2 |
| East Asian | 43.6% | 2 |
| Amish (not grpmax-eligible) | 39.8% | 3 |
| African / African-American | 33.3% | 3 |
| South Asian | 32.9% | 3 |
| Remaining individuals (not grpmax-eligible) | 28.5% | 4 |
| Ashkenazi Jewish (not grpmax-eligible) | 26.8% | 4 |
| European (non-Finnish) | 25.8% | 4 |
| Middle Eastern | 22.5% | 4 |
| Finnish (not grpmax-eligible) | 22.2% | 5 |

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**LRP2** population constraint: LOEUF 0.352, pLI 1, missense-Z 4.5356; ClinGen dosage — haploinsufficiency gene assoc. with recessive phenotype, triplosensitivity 0/3. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **congenital heart disease** — No Known Disease Relationship (AR)

## Protein context {#protein}

Residue **213** lies in the ldl-receptor class a 5 domain.

**4 experimental structure(s)** (PDB): [2M0P](https://www.rcsb.org/structure/2M0P), [9CWM](https://www.rcsb.org/structure/9CWM), [9I3V](https://www.rcsb.org/structure/9I3V), [9QAW](https://www.rcsb.org/structure/9QAW).

## What this gene does {#gene-function}

*Describes the biological roles of LRP2 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** LRP2's established molecular role includes calcium ion binding. p.Asp213= falls in the ldl-receptor class a 5 domain.


### Pathways affected {#pathways}

LRP2 participates in **5 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Cargo recognition for clathrin-mediated endocytosis](https://reactome.org/content/detail/R-HSA-8856825) | curated |
| [Clathrin-mediated endocytosis](https://reactome.org/content/detail/R-HSA-8856828) | curated |
| [Retinoid metabolism and transport](https://reactome.org/content/detail/R-HSA-975634) | curated |
| [Transport of RCbl within the body](https://reactome.org/content/detail/R-HSA-9758890) | curated |
| [Vitamin D (calciferol) metabolism](https://reactome.org/content/detail/R-HSA-196791) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** calcium ion binding, cargo receptor activity, protein-folding chaperone binding.

**Biological process:** receptor-mediated endocytosis, protein transport, metal ion transport, negative regulation of apoptotic process, phosphatidylinositol 3-kinase/protein kinase B signal transduction, response to leptin.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-02-04.

**Submitter consensus:** conflicting (7 Benign, 2 Likely benign).

**Submission history:** 9 submissions (2015–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| PreventionGenetics, part of Exact Sciences | Benign | criteria provided, single submitter | clinical testing |  |
| Illumina Laboratory Services, Illumina | Benign | criteria provided, single submitter | clinical testing | 2018-01-13 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |
| Genetic Services Laboratory, University of Chicago | Likely benign | no assertion criteria provided | clinical testing |  |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2015-03-03 |
| Genome-Nilou Lab | Benign | criteria provided, single submitter | clinical testing | 2021-07-15 |
| Mayo Clinic Laboratories, Mayo Clinic | Benign | criteria provided, single submitter | clinical testing | 2022-11-10 |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-04 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-11-26 |

## Associated conditions {#conditions}

[Donnai-Barrow syndrome](https://sugi.bio/atlas/disease/donnai-barrow-syndrome/).

**Reported phenotype names (ClinVar):** Donnai-Barrow syndrome, not specified, not provided, AllHighlyPenetrant, none provided, FACIOOCULOACOUSTICORENAL SYNDROME, DBS/FOAR SYNDROME.

## Similar variants {#similar}

Related LRP2 variant pages (same residue, condition, or type): [LRP2 c.12019+1G>A](/variant/lrp2-c-12019-plus-1g-a), [LRP2 c.2639+1G>A](/variant/lrp2-c-2639-plus-1g-a), [LRP2 c.3667+1G>A](/variant/lrp2-c-3667-plus-1g-a), [LRP2 c.8452+1G>A](/variant/lrp2-c-8452-plus-1g-a), [LRP2 p.Arg1953Ter](/variant/lrp2-p-arg1953ter), [LRP2 p.Arg2225Ter](/variant/lrp2-p-arg2225ter), [LRP2 p.Arg278Ter](/variant/lrp2-p-arg278ter), [LRP2 p.Arg3184Ter](/variant/lrp2-p-arg3184ter).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 129533). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*