# NM_015166.3(MLC1):c.-467G>A

https://sugi.bio/variant/mlc1-c-minus-467g-a

## Summary

**MLC1 c.-467G>A** is classified **Uncertain significance** in MLC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-12). Rare (popmax 0.347%, nfe); Associated with megalencephalic leukoencephalopathy with subcortical cysts 1.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs117812810 · 1 submitter · 1 linked condition · rare (popmax 0.347%, nfe)

## For patients & families {#patients}

This is a change in the MLC1 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to megalencephalic leukoencephalopathy with subcortical cysts 1.

*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, Autosomal recessive |
| Age of onset (of this condition) | Infancy, Neonatal |
| Clinical trials | 2 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | MLC1 is a diagnostic-grade gene on 10 Genomics England panels |

**Commonly reported features of Megalencephalic leukoencephalopathy with subcortical cysts** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Atypical behavior — Frequent (79-30%)
- Seizure — Frequent (79-30%)
- Ataxia — Frequent (79-30%)
- Spasticity — Frequent (79-30%)
- Mental deterioration — Frequent (79-30%)
- Unsteady gait — Frequent (79-30%)
- Motor deterioration — Frequent (79-30%)
- Postnatal macrocephaly — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0025430/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [MLC1](https://sugi.bio/atlas/gene/MLC1/) |
| Coding change (HGVS c.) | c.-467G>A |
| MANE Select transcript | [NM_015166](https://www.ncbi.nlm.nih.gov/nuccore/NM_015166) |
| dbSNP | [rs117812810](https://www.ncbi.nlm.nih.gov/snp/rs117812810/) |
| Variant type | single nucleotide variant |
| Location | chr22:50085762-50085762 (GRCh38) |
| ClinVar | [VCV342118](https://www.ncbi.nlm.nih.gov/clinvar/variation/342118/) |

**All HGVS expressions:** `NC_000022.10:g.50524191C>T`, `NC_000022.11:g.50085762C>T`, `NG_009162.1:g.5168G>A`, `NG_146516.1:g.789C>T`, `NM_001376473.1:c.-279G>A`, `NM_001376474.1:c.-60+43G>A`, `NM_001376475.1:c.-218+43G>A`, `NM_001376476.1:c.-121G>A`

## 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 -9.519, GERP -3.62 — fast-evolving / accelerated position
- CADD: **PHRED 0.052**. 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** — this absence is genuinely unknown. Where a position sits between the lowest and the highest record the release holds for its gene, an absent score is a result and we state it as one; this position falls outside them, or the gene has no scored position at all, so that test did not reach here. It may lie outside the scored MANE transcript scope, or it may have been scored with all four deltas below Δ0.2 just past the last surviving record. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.347%** (nfe) · FAF95 0.31% · FAF99 0.296% · 236/68,104 in the highest group · 308/152,570 alleles overall — rare (popmax 0.347%, nfe).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| European (non-Finnish) (grpmax) | 0.347% | 289 |
| Remaining individuals (not grpmax-eligible) | 0.235% | 425 |
| Amish (not grpmax-eligible) | 0.219% | 456 |
| Ashkenazi Jewish (not grpmax-eligible) | 0.173% | 578 |
| African / African-American | 0.0986% | 1,014 |
| Admixed American | 0.0849% | 1,177 |
| Finnish (not grpmax-eligible) | 0.047% | 2,126 |

*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}

**MLC1** population constraint: LOEUF 1.038, pLI 3.867e-09, missense-Z 0.44593; ClinGen dosage — haploinsufficiency gene assoc. with recessive phenotype, triplosensitivity Not yet evaluated/3. *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):

- **megalencephalic leukoencephalopathy with subcortical cysts 1** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 71.29, 31% of residues very-high.

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

*Describes the biological roles of MLC1 (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:** MLC1's established molecular role includes identical protein binding.


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

**Molecular function:** identical protein binding, protein-containing complex binding.

**Biological process:** positive regulation of intracellular transport, regulation of response to osmotic stress.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2018-01-12.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Uncertain significance | criteria provided, single submitter | clinical testing | 2018-01-12 |

## Associated conditions {#conditions}

[megalencephalic leukoencephalopathy with subcortical cysts 1](https://sugi.bio/atlas/disease/megalencephalic-leukoencephalopathy-with-subcortical-cysts-1/).

**Reported phenotype names (ClinVar):** Megalencephalic leukoencephalopathy with subcortical cysts 1, LEUKOENCEPHALOPATHY WITH SWELLING AND CYSTS, VACUOLATING MEGALENCEPHALIC LEUKOENCEPHALOPATHY WITH SUBCORTICAL CYSTS.

## Similar variants {#similar}

Related MLC1 variant pages (same residue, condition, or type): [MLC1 c.1059+1G>A](/variant/mlc1-c-1059-plus-1g-a), [MLC1 c.321+1G>A](/variant/mlc1-c-321-plus-1g-a), [MLC1 c.321+2T>C](/variant/mlc1-c-321-plus-2t-c), [MLC1 c.321+2T>G](/variant/mlc1-c-321-plus-2t-g), [MLC1 c.423+1G>A](/variant/mlc1-c-423-plus-1g-a), [MLC1 c.423+1G>T](/variant/mlc1-c-423-plus-1g-t), [MLC1 c.525+1G>A](/variant/mlc1-c-525-plus-1g-a), [MLC1 c.597+1G>A](/variant/mlc1-c-597-plus-1g-a).

### 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 342118). 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.*