# NM_006070.6(TFG):c.993C>T (p.Ala331=)

https://sugi.bio/variant/tfg-p-ala331

## Summary

**TFG p.Ala331= (c.993C>T)** is classified **Likely benign** in TFG (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-04). Very rare (popmax 0.00127%, nfe); Associated with hereditary motor and sensory neuropathy, Okinawa type.

**At a glance:** Likely benign · review: Single submitter · rsID rs1490621305 · 1 submitter · 2 linked conditions · very rare (popmax 0.00127%, nfe)

## For patients & families {#patients}

This is a change in the TFG gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to hereditary motor and sensory neuropathy, Okinawa type.

*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 dominant |
| Age of onset (of this condition) | Adult |
| Diagnostic panels | TFG is a diagnostic-grade gene on 9 Genomics England panels |

**Commonly reported features of Hereditary motor and sensory neuropathy, Okinawa type** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Areflexia — Very frequent (99-80%)
- Somatic sensory dysfunction — Very frequent (99-80%)
- Upper limb muscle weakness — Very frequent (99-80%)
- Lower limb muscle weakness — Very frequent (99-80%)
- Intermittent painful muscle spasms — Very frequent (99-80%)
- Cough — Very frequent (99-80%)
- Abnormal peripheral action potential amplitude — Very frequent (99-80%)
- Fatiguable weakness of proximal limb muscles — Very frequent (99-80%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0010131/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [TFG](https://sugi.bio/atlas/gene/TFG/) |
| Protein change (HGVS p.) | p.Ala331= |
| Coding change (HGVS c.) | c.993C>T |
| MANE Select transcript | [NM_006070](https://www.ncbi.nlm.nih.gov/nuccore/NM_006070) |
| dbSNP | [rs1490621305](https://www.ncbi.nlm.nih.gov/snp/rs1490621305/) |
| Variant type | single nucleotide variant |
| Location | chr3:100748321-100748321 (GRCh38) |
| ClinVar | [VCV1098041](https://www.ncbi.nlm.nih.gov/clinvar/variation/1098041/) |

**All HGVS expressions:** `NC_000003.11:g.100467165C>T`, `NC_000003.12:g.100748321C>T`, `NG_027821.2:g.44032C>T`, `NM_001007565.2:c.993C>T`, `NM_001195478.2:c.993C>T`, `NM_001195479.2:c.981C>T`, `NM_006070.6:c.993C>T`

## Computational & population evidence {#evidence}

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

- **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 1.746, phastCons 1 — 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 **0.00127%** (nfe) · FAF95 0.000763% · FAF99 0.000605% · 15/1,179,974 in the highest group · 15/1,461,828 alleles overall — very rare (popmax 0.00127%, nfe).

*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}

**TFG** population constraint: LOEUF 0.591, pLI 0.49485, missense-Z 1.3142. *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 **331** lies in the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 60.51, 21% of residues very-high.

**3 experimental structure(s)** (PDB): [8TEQ](https://www.rcsb.org/structure/8TEQ), [8TER](https://www.rcsb.org/structure/8TER), [9E7C](https://www.rcsb.org/structure/9E7C) — incl. mutant structure 8TEQ.

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

*Describes the biological roles of TFG (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:** TFG's established molecular role includes identical protein binding. p.Ala331= falls in the disordered region. In Reactome, TFG is annotated in disease pathway(s) including **Signaling by ALK fusions and activated point mutants**.

**Disease mechanism (Reactome):** TFG loss or alteration is curated in [Signaling by ALK fusions and activated point mutants](https://reactome.org/content/detail/R-HSA-9725370).

### Pathways affected {#pathways}

TFG participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Signaling by ALK fusions and activated point mutants](https://reactome.org/content/detail/R-HSA-9725370) | curated |
| [COPII-mediated vesicle transport](https://reactome.org/content/detail/R-HSA-204005) | curated |

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

**Molecular function:** identical protein binding.

**Biological process:** endoplasmic reticulum to Golgi vesicle-mediated transport.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-02-04.

**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 | 2023-02-04 |

## Associated conditions {#conditions}

[hereditary motor and sensory neuropathy, Okinawa type](https://sugi.bio/atlas/disease/hereditary-motor-and-sensory-neuropathy-okinawa-type/), [hereditary spastic paraplegia 57](https://sugi.bio/atlas/disease/hereditary-spastic-paraplegia-57/).

**Reported phenotype names (ClinVar):** Hereditary motor and sensory neuropathy, Okinawa type, Hereditary spastic paraplegia 57, HEREDITARY MOTOR AND SENSORY NEUROPATHY, PROXIMAL TYPE, Spastic paraplegia 57, autosomal recessive.

## Similar variants {#similar}

Related TFG variant pages (same residue, condition, or type): [TFG p.Arg106Cys](/variant/tfg-p-arg106cys), [TFG p.Arg22Trp](/variant/tfg-p-arg22trp), [TFG p.Pro285Leu](/variant/tfg-p-pro285leu), [TFG c.820+3G>A](/variant/tfg-c-820-plus-3g-a), [TFG p.Ala184Thr](/variant/tfg-p-ala184thr), [TFG p.Ala326Ser](/variant/tfg-p-ala326ser), [TFG p.Ala382Val](/variant/tfg-p-ala382val), [TFG p.Arg107Gln](/variant/tfg-p-arg107gln).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-06); 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 2026-07-14); 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 1098041). 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.*