# NM_144988.4(ALG14):c.179C>G (p.Ser60Cys)

https://sugi.bio/variant/alg14-p-ser60cys

## Summary

**ALG14 p.Ser60Cys (c.179C>G)** is classified **Uncertain significance** in ALG14 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-06-07). AlphaMissense: likely benign (0.1824); Ultra-rare (popmax 0.0713%, eas); Associated with myopathy, epilepsy, and progressive cerebral atrophy.

**At a glance:** Uncertain significance · review: Multiple submitters · rsID rs780277809 · 4 submitters · 3 linked conditions · AlphaMissense likely benign · ultra-rare (popmax 0.0713%, eas)

## For patients & families {#patients}

This is a change in the ALG14 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 4 submitters, and is linked to myopathy, epilepsy, and progressive cerebral atrophy.

*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.*

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0025813/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [ALG14](https://sugi.bio/atlas/gene/ALG14/) |
| Protein change (HGVS p.) | p.Ser60Cys |
| Coding change (HGVS c.) | c.179C>G |
| MANE Select transcript | [NM_144988](https://www.ncbi.nlm.nih.gov/nuccore/NM_144988) |
| dbSNP | [rs780277809](https://www.ncbi.nlm.nih.gov/snp/rs780277809/) |
| Variant type | single nucleotide variant |
| Location | chr1:95064975-95064975 (GRCh38) |
| ClinVar | [VCV390702](https://www.ncbi.nlm.nih.gov/clinvar/variation/390702/) |

**All HGVS expressions:** `NC_000001.10:g.95530531G>C`, `NC_000001.11:g.95064975G>C`, `NG_042044.1:g.12977C>G`, `NM_001305242.2:c.179C>G`, `NM_144988.4:c.179C>G`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.1824)
- REVEL 0.594 (indeterminate)
- SaProt LLR -10.714 (damaging) — differs from AlphaMissense
- → **In-silico consensus:** SaProt calls this damaging; AlphaMissense does not; REVEL makes no call
- Conservation: phyloP 9.725, GERP 2.43, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 27.4**. 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 (94,983,079–95,072,898), spanning 89,819 bp. Chi-square p 0.32. 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 **0.0713%** (eas) · FAF95 0.0519% · FAF99 0.0452% · 32/44,862 in the highest group · 77/1,613,454 alleles overall — ultra-rare (popmax 0.0713%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.0713% | 1,402 |
| Remaining individuals (not grpmax-eligible) | 0.0464% | 2,154 |
| Admixed American | 0.0233% | 4,285 |
| European (non-Finnish) | 0.00017% | 589,831 |

*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}

**ALG14** population constraint: LOEUF 1.055, pLI 7.0391e-05, missense-Z 0.019929. *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):

- **congenital disorder of glycosylation** — Limited (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 91.06, 74% of residues very-high.

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

*Describes the biological roles of ALG14 (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:** ALG14's established molecular role includes protein-membrane adaptor activity. In Reactome, ALG14 is annotated in disease pathway(s) including **Defective ALG14 causes ALG14-CMS**.

**Disease mechanism (Reactome):** ALG14 loss or alteration is curated in [Defective ALG14 causes ALG14-CMS](https://reactome.org/content/detail/R-HSA-5633231).

### Pathways affected {#pathways}

ALG14 participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective ALG14 causes ALG14-CMS](https://reactome.org/content/detail/R-HSA-5633231) | curated |
| [Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein](https://reactome.org/content/detail/R-HSA-446193) | curated |

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

**Molecular function:** protein-membrane adaptor activity.

**Biological process:** protein N-linked glycosylation, dolichol-linked oligosaccharide biosynthetic process.

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2024-06-07.

**Submitter consensus:** unanimous (6/6 Uncertain significance).

**Submission history:** 6 submissions (2016–2024); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Uncertain significance | criteria provided, single submitter | clinical testing | 2016-11-15 |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2022-07-15 |
| Genome-Nilou Lab | Uncertain significance | criteria provided, single submitter | clinical testing | 2023-04-11 |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-06-07 |

## Associated conditions {#conditions}

[myopathy, epilepsy, and progressive cerebral atrophy](https://sugi.bio/atlas/disease/myopathy-epilepsy-and-progressive-cerebral-atrophy/), [congenital myasthenic syndrome 15](https://sugi.bio/atlas/disease/congenital-myasthenic-syndrome-15/), [intellectual developmental disorder with epilepsy, behavioral abnormalities, and coarse facies](https://sugi.bio/atlas/disease/intellectual-developmental-disorder-with-epilepsy-behavioral-abnormalities-and-coarse-facies/).

**Reported phenotype names (ClinVar):** Myopathy, epilepsy, and progressive cerebral atrophy, not provided, Congenital myasthenic syndrome 15, Inborn genetic diseases, Intellectual developmental disorder with epilepsy, behavioral abnormalities, and coarse facies, Myasthenic syndrome, congenital, 15, without tubular aggregates, RECLASSIFIED - ADRA2C POLYMORPHISM, RECLASSIFIED - ADRB1 POLYMORPHISM, none provided.

## Similar variants {#similar}

Related ALG14 variant pages (same residue, condition, or type): [ALG14 p.Ala13Ser](/variant/alg14-p-ala13ser), [ALG14 p.Arg104Gln](/variant/alg14-p-arg104gln), [ALG14 p.Arg109Gln](/variant/alg14-p-arg109gln), [ALG14 p.Asn61Asp](/variant/alg14-p-asn61asp), [ALG14 p.Asn61Ser](/variant/alg14-p-asn61ser), [ALG14 p.Asn82Ser](/variant/alg14-p-asn82ser), [ALG14 p.Glu110Lys](/variant/alg14-p-glu110lys), [ALG14 p.Glu179Lys](/variant/alg14-p-glu179lys).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); 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 390702). 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.*