# NM_001008212.2(OPTN):c.441G>A (p.Val147=)

https://sugi.bio/variant/optn-p-val147

## Summary

**OPTN p.Val147= (c.441G>A)** is classified **Conflicting classifications of pathogenicity** in OPTN (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2026-01-26). Very rare (popmax 0.0011%, sas); Associated with Glaucoma 1, open angle, E.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs886046819 · 2 submitters · 3 linked conditions · very rare (popmax 0.0011%, sas)

## For patients & families {#patients}

This is a change in the OPTN gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 2 submitters, and is linked to Glaucoma 1, open angle, E.

*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:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [OPTN](https://sugi.bio/atlas/gene/OPTN/) |
| Protein change (HGVS p.) | p.Val147= |
| Coding change (HGVS c.) | c.441G>A |
| MANE Select transcript | [NM_001008212](https://www.ncbi.nlm.nih.gov/nuccore/NM_001008212) |
| dbSNP | [rs886046819](https://www.ncbi.nlm.nih.gov/snp/rs886046819/) |
| Variant type | single nucleotide variant |
| Location | chr10:13112524-13112524 (GRCh38) |
| ClinVar | [VCV299212](https://www.ncbi.nlm.nih.gov/clinvar/variation/299212/) |

**All HGVS expressions:** `NC_000010.10:g.13154524G>A`, `NC_000010.11:g.13112524G>A`, `NG_012876.1:g.17443G>A`, `NM_001008211.1:c.441G>A`, `NM_001008212.2:c.441G>A`, `NM_001008213.1:c.441G>A`, `NM_021980.4:c.441G>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 3.278, GERP 0.5, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 5.358**. 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: **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 OPTN (957 scored positions, the nearest 61 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 (gnomAD v4.1): grpmax **0.0011%** (sas) · FAF95 6.8e-05% · FAF99 1.9e-05% · 1/91,078 in the highest group · 4/1,614,118 alleles overall — very rare (popmax 0.0011%, sas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| South Asian (grpmax) | 0.0011% | 91,078 |
| European (non-Finnish) | 0.000254% | 393,340 |

*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}

**OPTN** population constraint: LOEUF 0.877, pLI 9.8571e-10, missense-Z 1.2212. *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):

- **amyotrophic lateral sclerosis type 12** — Definitive (SD)
- **glaucoma, normal tension, susceptibility to** — Definitive (AD)

## Protein context {#protein}

Residue **147** lies in the 'interaction with rab8' region; an α-helix.

AlphaFold model confidence (whole protein): pLDDT 77.90, 53% of residues very-high.

**14 experimental structure(s)** (PDB): [2LO4](https://www.rcsb.org/structure/2LO4), [2LUE](https://www.rcsb.org/structure/2LUE), [3VTV](https://www.rcsb.org/structure/3VTV), [3VTW](https://www.rcsb.org/structure/3VTW), [5AAZ](https://www.rcsb.org/structure/5AAZ), [5B83](https://www.rcsb.org/structure/5B83) — incl. mutant structure 5EOA.

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

*Describes the biological roles of OPTN (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:** OPTN's established molecular role includes protein-macromolecule adaptor activity. p.Val147= falls in the interaction with rab8 region.


### Pathways affected {#pathways}

OPTN participates in **10 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE)](https://reactome.org/content/detail/R-HSA-936964) | curated |
| [PINK1-PRKN Mediated Mitophagy](https://reactome.org/content/detail/R-HSA-5205685) | curated |
| [Regulation of PLK1 Activity at G2/M Transition](https://reactome.org/content/detail/R-HSA-2565942) | curated |
| [Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 ](https://reactome.org/content/detail/R-HSA-9824878) | curated |
| [Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation](https://reactome.org/content/detail/R-HSA-9828211) | curated |
| [Regulation of TNFR1 signaling](https://reactome.org/content/detail/R-HSA-5357905) | curated |
| [TBC/RABGAPs](https://reactome.org/content/detail/R-HSA-8854214) | curated |
| [TICAM1-dependent activation of IRF3/IRF7](https://reactome.org/content/detail/R-HSA-9013973) | curated |
| [TNFR1-induced NF-kappa-B signaling pathway](https://reactome.org/content/detail/R-HSA-5357956) | curated |
| [TNFR1-induced proapoptotic signaling](https://reactome.org/content/detail/R-HSA-5357786) | curated |

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

**Molecular function:** protein-macromolecule adaptor activity, polyubiquitin modification-dependent protein binding, identical protein binding.

**Biological process:** negative regulation of receptor recycling, Golgi organization, positive regulation of autophagy, protein localization to Golgi apparatus, cellular response to unfolded protein, Golgi to plasma membrane protein transport.

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2026-01-26.

**Submitter consensus:** conflicting (2 Uncertain significance, 1 Likely benign).

**Submission history:** 3 submissions (2018–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Uncertain significance | criteria provided, single submitter | clinical testing | 2018-01-12 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2026-01-26 |

## Associated conditions {#conditions}

[Glaucoma 1, open angle, E](https://sugi.bio/atlas/disease/glaucoma-1-open-angle-e/), [amyotrophic lateral sclerosis type 12](https://sugi.bio/atlas/disease/amyotrophic-lateral-sclerosis-type-12/), [OPTN-related open angle glaucoma](https://sugi.bio/atlas/disease/optn-related-open-angle-glaucoma/).

**Reported phenotype names (ClinVar):** Glaucoma 1, open angle, E, Primary open angle glaucoma, Amyotrophic lateral sclerosis type 12, AMYOTROPHIC LATERAL SCLEROSIS 12 WITH OR WITHOUT FRONTOTEMPORAL DEMENTIA, OPTN-related open angle glaucoma.

## Similar variants {#similar}

Related OPTN variant pages (same residue, condition, or type): [OPTN p.Val147Glu](/variant/optn-p-val147glu), [OPTN p.Val147Ala](/variant/optn-p-val147ala), [OPTN p.Val147Leu](/variant/optn-p-val147leu), [OPTN c.1149-2A>G](/variant/optn-c-1149-minus-2a-g), [OPTN c.626+1G>A](/variant/optn-c-626-plus-1g-a), [OPTN c.780-2A>C](/variant/optn-c-780-minus-2a-c), [OPTN p.Gln165Ter](/variant/optn-p-gln165ter), [OPTN p.Gln335Ter](/variant/optn-p-gln335ter).

### 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 299212). 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.*