# NM_001195248.2(APTX):c.229dup (p.Gln77fs)

https://sugi.bio/variant/aptx-p-gln77fs

## Summary

**APTX p.Gln77fs (c.229dup)** is classified **Pathogenic** in APTX (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-15). No gnomAD frequency available for this variant.

**At a glance:** Pathogenic · review: Single submitter · rsID rs2489584021 · 1 submitter · no gnomAD frequency available for this variant

## For patients & families {#patients}

This is a change in the APTX gene that is reported as disease-causing, but on limited review, submitted by 1 submitter.

*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 | [APTX](https://sugi.bio/atlas/gene/APTX/) |
| Protein change (HGVS p.) | p.Gln77fs |
| Coding change (HGVS c.) | c.229dup |
| MANE Select transcript | [NM_001195248](https://www.ncbi.nlm.nih.gov/nuccore/NM_001195248) |
| dbSNP | [rs2489584021](https://www.ncbi.nlm.nih.gov/snp/rs2489584021/) |
| Variant type | Duplication |
| Location | chr9:32987797-32987798 (GRCh38) |
| ClinVar | [VCV2821016](https://www.ncbi.nlm.nih.gov/clinvar/variation/2821016/) |

**All HGVS expressions:** `NC_000009.11:g.32987797dup`, `NC_000009.12:g.32987799dup`, `NG_012821.2:g.42334dup`, `NM_001195248.2:c.229dup`, `NM_001195249.2:c.229dup`, `NM_001195250.2:c.134-67dup`, `NM_001195251.2:c.229dup`, `NM_001195252.2:c.229dup`, `NM_001195254.2:c.134-67dup`, `NM_001368995.1:c.229dup`, `NM_001368996.1:c.229dup`, `NM_001368997.1:c.229dup`, `NM_001368998.1:c.229dup`, `NM_001368999.1:c.229dup`, `NM_001369000.1:c.134-67dup`, `NM_001369001.1:c.134-67dup`, `NM_001369002.1:c.-36dup`, `NM_001369003.1:c.-36dup`, `NM_001369004.1:c.-36dup`, `NM_001369005.1:c.-36dup`, `NM_001369006.1:c.-36dup`, `NM_001370669.1:c.-36dup`, `NM_001370670.1:c.-36dup`, `NM_001370673.1:c.-36dup`, `NM_175069.3:c.229dup`, `NM_175073.3:c.229dup`, `NR_036576.1:n.302dup`, `NR_036578.1:n.324dup`, `NR_036579.1:n.471dup`, `NR_160920.1:n.295dup`, `NR_160927.1:n.545dup`, `NR_160929.1:n.349dup`

## Computational & population evidence {#evidence}

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

- **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 2.825, GERP 0.583, phastCons 1 — highly conserved position (PP3-type support)
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 0.973, pLI 2.0655e-07. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 4 of 8**, so the transcript is predicted to undergo NMD.
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no duplication variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency: **no gnomAD frequency available for this variant** — rarity (ACMG PM2) and BA1/BS1 cannot be assessed for this variant.

*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}

**APTX** population constraint: LOEUF 0.973, pLI 2.0655e-07, missense-Z 0.27421. *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 **77** lies in the fha-like domain; the 'interactions with adprt/parp1 and ncl' region; a β-strand.

AlphaFold model confidence (whole protein): pLDDT 81.52, 64% of residues very-high.

**11 experimental structure(s)** (PDB): [3KT9](https://www.rcsb.org/structure/3KT9), [4NDF](https://www.rcsb.org/structure/4NDF), [4NDG](https://www.rcsb.org/structure/4NDG), [4NDH](https://www.rcsb.org/structure/4NDH), [4NDI](https://www.rcsb.org/structure/4NDI), [6CVO](https://www.rcsb.org/structure/6CVO) — incl. mutant structure 4NDI.

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

*Describes the biological roles of APTX (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:** APTX's established molecular role includes chromatin binding. p.Gln77fs falls in the fha-like domain.


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

**Molecular function:** chromatin binding, damaged DNA binding, double-stranded DNA binding, double-stranded RNA binding, phosphoglycolate phosphatase activity, DNA 5'-adenosine monophosphate hydrolase activity.

**Biological process:** single strand break repair, regulation of protein stability.

## Clinical significance {#significance}

**Pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-12-15.

**Submitter consensus:** unanimous (1/1 Pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2022-12-15 |

**Reported phenotype names (ClinVar):** not provided, none provided.

## Similar variants {#similar}

Related APTX variant pages (same residue, condition, or type): [APTX c.484-3dup](/variant/aptx-c-484-minus-3dup), [APTX c.771-12dup](/variant/aptx-c-771-minus-12dup), [APTX c.771-13_771-12dup](/variant/aptx-c-771-minus-13-771-minus-12dup), [APTX p.Ala198fs](/variant/aptx-p-ala198fs), [APTX p.Glu232fs](/variant/aptx-p-glu232fs), [APTX p.Gly137fs](/variant/aptx-p-gly137fs), [APTX c.133+18dup](/variant/aptx-c-133-plus-18dup), [APTX c.484-14dup](/variant/aptx-c-484-minus-14dup).

### 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 2821016). 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.*