# NM_001081.4(CUBN):c.265A>C (p.Lys89Gln)

https://sugi.bio/variant/cubn-p-lys89gln

## Summary

**CUBN p.Lys89Gln (c.265A>C)** is classified **Uncertain significance** in CUBN (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-04-13). AlphaMissense: likely benign (0.1512); Very rare (popmax 0.00268%, afr); Associated with Imerslund-Grasbeck syndrome.

**At a glance:** Uncertain significance · review: Multiple submitters · rsID rs755860454 · 2 submitters · 2 linked conditions · AlphaMissense likely benign · very rare (popmax 0.00268%, afr)

## For patients & families {#patients}

This is a change in the CUBN gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 2 submitters, and is linked to Imerslund-Grasbeck 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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | Childhood |
| Prevalence | 1-9 / 1 000 000 (Finland) |
| Diagnostic panels | CUBN is a diagnostic-grade gene on 11 Genomics England panels |

**Commonly reported features of Imerslund-Gräsbeck syndrome** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Decreased circulating vitamin B12 concentration — Obligate (100%)
- Malabsorption of Vitamin B12 — Obligate (100%)
- Abnormal blood 5-methyltetrahydrofolate level — Obligate (100%)
- Megaloblastic anemia — Very frequent (99-80%)
- Macrocytic anemia — Very frequent (99-80%)
- Hypersegmentation of neutrophil nuclei — Very frequent (99-80%)
- Proteinuria — Frequent (79-30%)
- Pallor — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0007006/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CUBN](https://sugi.bio/atlas/gene/CUBN/) |
| Protein change (HGVS p.) | p.Lys89Gln |
| Coding change (HGVS c.) | c.265A>C |
| MANE Select transcript | [NM_001081](https://www.ncbi.nlm.nih.gov/nuccore/NM_001081) |
| dbSNP | [rs755860454](https://www.ncbi.nlm.nih.gov/snp/rs755860454/) |
| Variant type | single nucleotide variant |
| Location | chr10:17127912-17127912 (GRCh38) |
| ClinVar | [VCV1029049](https://www.ncbi.nlm.nih.gov/clinvar/variation/1029049/) |

**All HGVS expressions:** `LRG_540:g.6906A>C`, `LRG_540t1:c.265A>C`, `NC_000010.10:g.17169911T>G`, `NC_000010.11:g.17127912T>G`, `NG_008967.1:g.6906A>C`, `NM_001081.4:c.265A>C`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- AlphaMissense **likely benign** (0.1512)
- REVEL 0.452 (indeterminate)
- Conservation: phyloP 4.92, GERP 1.71, phastCons 1 — highly conserved (differs from AlphaMissense)
- **SaProt:** not scored — SaProt is structure-aware and AlphaFold DB has no model for this protein. That is a property of the dataset, not of the variant, and is not evidence either way.
- CADD: **PHRED 24.2**. 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.*
- Regional missense constraint: **o/e 1.04** across the covering region of the MANE Select transcript (17,045,981–17,129,765), spanning 83,784 bp. Chi-square p 0.11. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code 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 **0.00268%** (afr) · FAF95 0.000444% · FAF99 0.000166% · 2/74,690 in the highest group · 3/1,602,520 alleles overall — very rare (popmax 0.00268%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.00268% | 37,345 |
| Remaining individuals (not grpmax-eligible) | 0.00161% | 62,120 |

*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}

**CUBN** population constraint: LOEUF 0.756, pLI 1.0686e-57, missense-Z 1.0005; 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.*

## Protein context {#protein}

Residue **89** lies in an α-helix.

**2 experimental structure(s)** (PDB): [3KQ4](https://www.rcsb.org/structure/3KQ4), [6GJE](https://www.rcsb.org/structure/6GJE).

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

*Describes the biological roles of CUBN (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:** CUBN's established molecular role includes cargo receptor activity. In Reactome, CUBN is annotated in disease pathway(s) including **Defective AMN causes MGA1**, **Defective CUBN causes MGA1**.

**Disease mechanism (Reactome):** CUBN loss or alteration is curated in [Defective AMN causes MGA1](https://reactome.org/content/detail/R-HSA-3359462), [Defective CUBN causes MGA1](https://reactome.org/content/detail/R-HSA-3359463).

### Pathways affected {#pathways}

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

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective AMN causes MGA1](https://reactome.org/content/detail/R-HSA-3359462) | curated |
| ⚕ [Defective CUBN causes MGA1](https://reactome.org/content/detail/R-HSA-3359463) | curated |
| [HDL clearance](https://reactome.org/content/detail/R-HSA-8964011) | curated |
| [Uptake of dietary cobalamins into enterocytes](https://reactome.org/content/detail/R-HSA-9758881) | curated |
| [Vitamin D (calciferol) metabolism](https://reactome.org/content/detail/R-HSA-196791) | curated |

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

**Molecular function:** cargo receptor activity, protein homodimerization activity.

**Biological process:** cobalamin metabolic process, cobalamin transport.

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2023-04-13.

**Submitter consensus:** unanimous (2/2 Uncertain significance).

**Submission history:** 2 submissions (2020–2023); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Baylor Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2020-06-20 |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2023-04-13 |

## Associated conditions {#conditions}

[Imerslund-Grasbeck syndrome](https://sugi.bio/atlas/disease/imerslund-grasbeck-syndrome/), [Imerslund-Grasbeck syndrome type 1](https://sugi.bio/atlas/disease/imerslund-grasbeck-syndrome-type-1/).

**Reported phenotype names (ClinVar):** Imerslund-Grasbeck syndrome, Imerslund-Grasbeck syndrome type 1, Imerslund-Gräsbeck syndrome, ENTEROCYTE COBALAMIN MALABSORPTION, ENTEROCYTE INTRINSIC FACTOR RECEPTOR, DEFECT OF, PERNICIOUS ANEMIA, JUVENILE, DUE TO SELECTIVE INTESTINAL MALABSORPTION OF VITAMIN B12, WITH PROTEINURIA, Megaloblastic anemia due to inborn errors of metabolism, Megaloblastic anemia 1, Finnish type, Imerslund-Gräsbeck syndrome 1, MEGALOBLASTIC ANEMIA, 1.

## Similar variants {#similar}

Related CUBN variant pages (same residue, condition, or type): [CUBN c.10033-1G>A](/variant/cubn-c-10033-minus-1g-a), [CUBN c.1230+1G>A](/variant/cubn-c-1230-plus-1g-a), [CUBN c.3672+2T>C](/variant/cubn-c-3672-plus-2t-c), [CUBN c.3829+1G>A](/variant/cubn-c-3829-plus-1g-a), [CUBN c.4350+2T>C](/variant/cubn-c-4350-plus-2t-c), [CUBN c.6821+3A>G](/variant/cubn-c-6821-plus-3a-g), [CUBN c.6822-1G>A](/variant/cubn-c-6822-minus-1g-a), [CUBN c.8598+1G>T](/variant/cubn-c-8598-plus-1g-t).

### 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 1029049). 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.*