# NM_024301.5(FKRP):c.1036T>C (p.Ser346Pro)

https://sugi.bio/variant/fkrp-p-ser346pro

## Summary

**FKRP p.Ser346Pro (c.1036T>C)** is classified **Likely pathogenic** in FKRP (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely pathogenic (0.9858); Absent from gnomAD v4.1; Associated with autosomal recessive limb-girdle muscular dystrophy type 2I.

**At a glance:** Likely pathogenic · review: No assertion criteria · rsID rs753811189 · 1 submitter · 1 linked condition · AlphaMissense likely pathogenic · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the FKRP gene that is considered likely disease-causing, submitted by 1 submitter, and is linked to autosomal recessive limb-girdle muscular dystrophy type 2I.

*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) | Adolescent, Adult, Childhood |
| Prevalence | 1-9 / 100 000 (Europe) |
| Clinical trials | 9 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | FKRP is a diagnostic-grade gene on 21 Genomics England panels |

**Commonly reported features of FKRP-related limb-girdle muscular dystrophy R9** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Elevated circulating creatine kinase concentration — Very frequent (99-80%)
- Muscular dystrophy — Very frequent (99-80%)
- Proximal muscle weakness — Very frequent (99-80%)
- Reduced muscle fiber alpha dystroglycan — Very frequent (99-80%)
- Generalized hypotonia — Frequent (79-30%)
- Waddling gait — Frequent (79-30%)
- Shoulder girdle muscle weakness — Frequent (79-30%)
- Pelvic girdle muscle weakness — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0012533/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [FKRP](https://sugi.bio/atlas/gene/FKRP/) |
| Protein change (HGVS p.) | p.Ser346Pro |
| Coding change (HGVS c.) | c.1036T>C |
| MANE Select transcript | [NM_024301](https://www.ncbi.nlm.nih.gov/nuccore/NM_024301) |
| dbSNP | [rs753811189](https://www.ncbi.nlm.nih.gov/snp/rs753811189/) |
| Variant type | single nucleotide variant |
| Location | chr19:46756486-46756486 (GRCh38) |
| ClinVar | [VCV487485](https://www.ncbi.nlm.nih.gov/clinvar/variation/487485/) |

**All HGVS expressions:** `LRG_761:g.15441T>C`, `LRG_761t1:c.1036T>C`, `NC_000019.10:g.46756486T>C`, `NC_000019.9:g.47259743T>C`, `NG_008898.2:g.15441T>C`, `NM_001039885.3:c.1036T>C`, `NM_024301.5:c.1036T>C`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.9858) — concordant with the pathogenic call
- REVEL 0.813 (moderately pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -13.123 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this damaging
- Conservation: phyloP 4.952, GERP 0.292, phastCons 1 — highly conserved (agrees)
- AlphaMissense ranks this among the **top 7%** most-pathogenic-predicted substitutions in FKRP (of 2,872 modeled).
- CADD: **PHRED 26.1**. 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 1.06** across the covering region of the MANE Select transcript (46,755,451–46,756,935), spanning 1,484 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: **no splice effect predicted**. SpliceAI outputs four numbers per variant, not one: acceptor loss, donor loss, acceptor gain, donor gain (DS_AL / DS_DL / DS_AG / DS_DG). A loss score is an existing splice site weakened or destroyed; a gain score is a new site created or an existing one strengthened. The release publishes its own filter rule, which we read from the dataset rather than assume: an allele is reported only if the largest of its four deltas reaches 0.2. No allele at this position is in the release, so all four are under 0.2 for every alternate allele here. No figure is shown because none was read: the bound is deduced from that absence. It is a result, not a gap in our data, because the release scores every possible substitution across the transcripts it covers (Ensembl MANE v1.4) before it filters, so what survives for a gene is one continuous stretch. What is measured is that this position sits inside the stretch covered for FKRP (283 scored positions, the nearest 951 bases away); what is taken from the release's own description, rather than measured, is that coverage inside that stretch is continuous. On that, SpliceAI did score it. *ClinGen's SVI treats the largest of the four as evidence against a splicing effect at or below 0.1, where it may support BP4, and as uninformative between 0.1 and 0.2. We cannot tell which applies here, so these SpliceAI data support neither BP4 nor PP3; that is a statement about this evidence alone, not about the variant's other evidence.*
- Population frequency: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*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}

**FKRP** population constraint: LOEUF 1.543, pLI 6.1822e-10, missense-Z -2.4908. *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):

- **myopathy caused by variation in FKRP** — Definitive (AR)

## Protein context {#protein}

Residue **346** lies in an α-helix.

AlphaFold model confidence (whole protein): pLDDT 94.08, 86% of residues very-high.

**8 experimental structure(s)** (PDB): [6KAJ](https://www.rcsb.org/structure/6KAJ), [6KAK](https://www.rcsb.org/structure/6KAK), [6KAL](https://www.rcsb.org/structure/6KAL), [6KAM](https://www.rcsb.org/structure/6KAM), [6KAN](https://www.rcsb.org/structure/6KAN), [6L7S](https://www.rcsb.org/structure/6L7S).

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

*Describes the biological roles of FKRP (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:** FKRP's established molecular role includes phosphotransferase activity, for other substituted phosphate groups.


### Pathways affected {#pathways}

FKRP participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Matriglycan biosynthesis on DAG1](https://reactome.org/content/detail/R-HSA-9939291) | curated |

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

**Molecular function:** phosphotransferase activity, for other substituted phosphate groups, identical protein binding.

**Biological process:** protein O-linked glycosylation via mannose, protein tetramerization.

## Clinical significance {#significance}

**Likely pathogenic** — review status No assertion criteria *(no assertion criteria provided)*.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Institute of Human Genetics, Cologne University | Likely pathogenic | no assertion criteria provided | clinical testing |  |

## Associated conditions {#conditions}

[autosomal recessive limb-girdle muscular dystrophy type 2I](https://sugi.bio/atlas/disease/autosomal-recessive-limb-girdle-muscular-dystrophy-type-2i/).

**Reported phenotype names (ClinVar):** Autosomal recessive limb-girdle muscular dystrophy type 2I, MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2I, MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY, LIMB-GIRDLE, FRKP-RELATED, MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY (LIMB-GIRDLE), TYPE C, 5.

## Similar variants {#similar}

Related FKRP variant pages (same residue, condition, or type): [FKRP p.Ser346=](/variant/fkrp-p-ser346), [FKRP p.Ser346Leu](/variant/fkrp-p-ser346leu), [FKRP p.Ala455Asp](/variant/fkrp-p-ala455asp), [FKRP p.Arg176Ter](/variant/fkrp-p-arg176ter), [FKRP p.Arg275Cys](/variant/fkrp-p-arg275cys), [FKRP p.Asn463Asp](/variant/fkrp-p-asn463asp), [FKRP p.Gln105Ter](/variant/fkrp-p-gln105ter), [FKRP p.Gln406Ter](/variant/fkrp-p-gln406ter).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); 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 487485). 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.*