# NM_000404.4(GLB1):c.5C>G (p.Pro2Arg)

https://sugi.bio/variant/glb1-p-pro2arg

## Summary

**GLB1 p.Pro2Arg (c.5C>G)** is classified **Likely benign** in GLB1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-22). AlphaMissense: likely benign (0.0666); Ultra-rare (popmax 0.0551%, amr); Associated with mucopolysaccharidosis type 4B.

**At a glance:** Likely benign · review: Single submitter · rsID rs779544911 · 1 submitter · 2 linked conditions · AlphaMissense likely benign · ultra-rare (popmax 0.0551%, amr)

> **Built without this gene's context.** ClinVar files this variant under an overlapping gene, so its own gene's record set does not contain it and this page is assembled from the variant alone. Gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up — absent from this page, not from the data.

## For patients & families {#patients}

This is a change in the GLB1 gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to mucopolysaccharidosis type 4B.

*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, Infancy |
| Prevalence | <1 / 1 000 000 (Sweden) |

**Commonly reported features of Mucopolysaccharidosis type 4** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Abnormality of the dentition — Very frequent (99-80%)
- Hearing impairment — Very frequent (99-80%)
- Short neck — Very frequent (99-80%)
- Pectus carinatum — Very frequent (99-80%)
- Abnormal rib morphology — Very frequent (99-80%)
- Abnormal metaphysis morphology — Very frequent (99-80%)
- Gait disturbance — Very frequent (99-80%)
- Delayed skeletal maturation — Very frequent (99-80%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0003786/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [GLB1](https://sugi.bio/atlas/gene/GLB1/) |
| Protein change (HGVS p.) | p.Pro2Arg |
| Coding change (HGVS c.) | c.5C>G |
| MANE Select transcript | [NM_000404](https://www.ncbi.nlm.nih.gov/nuccore/NM_000404) |
| dbSNP | [rs779544911](https://www.ncbi.nlm.nih.gov/snp/rs779544911/) |
| Variant type | single nucleotide variant |
| Location | chr3:33097081-33097081 (GRCh38) |
| ClinVar | [VCV972610](https://www.ncbi.nlm.nih.gov/clinvar/variation/972610/) |

**All HGVS expressions:** `NC_000003.11:g.33138573G>C`, `NC_000003.12:g.33097081G>C`, `NG_009005.1:g.5122C>G`, `NG_009005.2:g.5065C>G`, `NG_169445.1:g.448G>C`, `NM_000404.4:c.5C>G`, `NM_001039770.3:c.-471C>G`, `NM_001135602.3:c.5C>G`, `NM_001136238.2:c.-367C>G`, `NM_001317040.2:c.5C>G`, `NM_001393580.1:c.5C>G`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.0666)
- REVEL 0.32 (indeterminate)
- SaProt LLR -6.312 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate
- Conservation: phyloP -2.962, GERP -3.49 — fast-evolving / accelerated position
- CADD: **PHRED 5.369**. 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 0.93** across the covering region of the MANE Select transcript (32,997,048–33,097,085), spanning 100,037 bp. Chi-square p 0.044. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not looked up on this page** — it was served without the gene's SpliceAI index, so no lookup was made. This is a gap in this page, not in the data, and says nothing about whether a splicing effect is predicted.
- Population frequency (gnomAD v4.1): grpmax **0.0551%** (amr) · FAF95 0.0403% · FAF99 0.0352% · 33/59,876 in the highest group · 33/1,612,428 alleles overall — ultra-rare (popmax 0.0551%, amr).

*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.*

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-10-22.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2025-10-22 |

## Associated conditions {#conditions}

[mucopolysaccharidosis type 4B](https://sugi.bio/atlas/disease/mucopolysaccharidosis-type-4b/), [GM1 gangliosidosis](https://sugi.bio/atlas/disease/gm1-gangliosidosis/).

**Reported phenotype names (ClinVar):** Mucopolysaccharidosis, MPS-IV-B, GM1 gangliosidosis, Mucopolysaccharidosis type IV B, Mucopolysaccharidosis Type IVB (Morquio B Disease), MORQUIO SYNDROME B, Mucopolysaccharidosis type 4B, Mucopolysaccharidosis Type IVB, Mucopolysaccharidosis type IVB (Morquio), MPS IVB.

### 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 972610). 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.*