# NM_006302.3(MOGS):c.329G>A (p.Arg110His)

https://sugi.bio/variant/mogs-p-arg110his

## Summary

**MOGS p.Arg110His (c.329G>A)** is classified **Likely pathogenic** in MOGS (ClinVar, No assertion criteria, 1 submitter; last evaluated 2015-03-01). AlphaMissense: likely pathogenic (0.6154); Very rare (popmax 0.00225%, eas); Associated with MOGS-congenital disorder of glycosylation.

**At a glance:** Likely pathogenic · review: No assertion criteria · rsID rs863225089 · 1 submitter · 1 linked condition · AlphaMissense likely pathogenic · very rare (popmax 0.00225%, eas)

## For patients & families {#patients}

This is a change in the MOGS gene that is considered likely disease-causing, submitted by 1 submitter, and is linked to MOGS-congenital disorder of glycosylation.

*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) | Infancy, Neonatal |
| Diagnostic panels | MOGS is a diagnostic-grade gene on 14 Genomics England panels |

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

- Retrognathia — Frequent (79-30%)
- Wide nose — Frequent (79-30%)
- Long eyelashes — Frequent (79-30%)
- Hirsutism — Frequent (79-30%)
- Seizure — Frequent (79-30%)
- Abnormal facial shape — Frequent (79-30%)
- Decreased circulating IgA level — Frequent (79-30%)
- Decreased circulating total IgM — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0010767/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [MOGS](https://sugi.bio/atlas/gene/MOGS/) |
| Protein change (HGVS p.) | p.Arg110His |
| Coding change (HGVS c.) | c.329G>A |
| MANE Select transcript | [NM_006302](https://www.ncbi.nlm.nih.gov/nuccore/NM_006302) |
| dbSNP | [rs863225089](https://www.ncbi.nlm.nih.gov/snp/rs863225089/) |
| Variant type | single nucleotide variant |
| Location | chr2:74464919-74464919 (GRCh38) |
| ClinVar | [VCV217735](https://www.ncbi.nlm.nih.gov/clinvar/variation/217735/) |

**All HGVS expressions:** `LRG_1226:g.5492G>A`, `LRG_1226t1:c.329G>A`, `NC_000002.11:g.74692046C>T`, `NC_000002.12:g.74464919C>T`, `NG_008922.1:g.5492G>A`, `NM_001146158.2:c.11G>A`, `NM_006302.3:c.329G>A`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- AlphaMissense **likely pathogenic** (0.6154) — concordant with the pathogenic call
- REVEL 0.53 (indeterminate)
- SaProt LLR -12.418 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt both call this damaging; REVEL is indeterminate
- Conservation: phyloP 7.656, GERP 1.36, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 31.0**. 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 0.99** across the covering region of the MANE Select transcript (74,462,489–74,465,247), spanning 2,758 bp. Chi-square p 0.9. 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 **0.00225%** (eas) · 1/44,518 in the highest group · 2/1,604,276 alleles overall — very rare (popmax 0.00225%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.00225% | 44,518 |
| European (non-Finnish) | 8.51e-05% | 1,175,054 |

*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}

**MOGS** population constraint: LOEUF 0.85, pLI 2.6946e-10, missense-Z 0.86484. *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):

- **MOGS-congenital disorder of glycosylation** — Definitive (AR)

## Protein context {#protein}

Residue **110** lies in the 'required for endoplasmic reticulum targeting' region.

AlphaFold model confidence (whole protein): pLDDT 92.42, 86% of residues very-high.

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

*Describes the biological roles of MOGS (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:** p.Arg110His falls in the required for endoplasmic reticulum targeting region. In Reactome, MOGS is annotated in disease pathway(s) including **Defective MOGS causes CDG-2b**, **Maturation of spike protein**.

**Disease mechanism (Reactome):** MOGS loss or alteration is curated in [Defective MOGS causes CDG-2b](https://reactome.org/content/detail/R-HSA-4793954), [Maturation of spike protein](https://reactome.org/content/detail/R-HSA-9683686), [Maturation of spike protein](https://reactome.org/content/detail/R-HSA-9694548).

### Pathways affected {#pathways}

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

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective MOGS causes CDG-2b](https://reactome.org/content/detail/R-HSA-4793954) | curated |
| ⚕ [Maturation of spike protein](https://reactome.org/content/detail/R-HSA-9683686) | curated |
| ⚕ [Maturation of spike protein](https://reactome.org/content/detail/R-HSA-9694548) | curated |
| [N-glycan trimming in the ER and Calnexin/Calreticulin cycle](https://reactome.org/content/detail/R-HSA-532668) | curated |
| [Regulation of CDH1 posttranslational processing and trafficking to plasma membrane](https://reactome.org/content/detail/R-HSA-9768727) | curated |

## Clinical significance {#significance}

**Likely pathogenic** — review status No assertion criteria *(no assertion criteria provided)*, last evaluated 2015-03-01.

**Submitter consensus:** unanimous (1/1 Likely pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Undiagnosed Diseases Program Translational Research Laboratory, National Institutes of Health | Likely pathogenic | no assertion criteria provided | research | 2015-03-01 |

## Associated conditions {#conditions}

[MOGS-congenital disorder of glycosylation](https://sugi.bio/atlas/disease/mogs-congenital-disorder-of-glycosylation/).

**Reported phenotype names (ClinVar):** MOGS-congenital disorder of glycosylation, CDG 2B, MOGS-CDG, CDG IIb, GLUCOSIDASE I DEFICIENCY.

## Similar variants {#similar}

Related MOGS variant pages (same residue, condition, or type): [MOGS p.Arg110=](/variant/mogs-p-arg110), [MOGS p.Arg110Gly](/variant/mogs-p-arg110gly), [MOGS p.Arg495Ter](/variant/mogs-p-arg495ter), [MOGS p.Gln124Ter](/variant/mogs-p-gln124ter), [MOGS p.Gln505Ter](/variant/mogs-p-gln505ter), [MOGS p.Ala22Glu](/variant/mogs-p-ala22glu), [MOGS p.Ala292Asp](/variant/mogs-p-ala292asp), [MOGS p.Ala292Pro](/variant/mogs-p-ala292pro).

### 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 217735). 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.*