# NM_001195248.2(APTX):c.588_595del (p.Lys197fs)

https://sugi.bio/variant/aptx-p-lys197fs

## Summary

**APTX p.Lys197fs (c.588_595del)** is classified **Pathogenic** in APTX (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-29). Very rare (popmax 0.00134%, afr).

**At a glance:** Pathogenic · review: Single submitter · rsID rs1563961179 · 1 submitter · very rare (popmax 0.00134%, afr)

## 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.Lys197fs |
| Coding change (HGVS c.) | c.588_595del |
| MANE Select transcript | [NM_001195248](https://www.ncbi.nlm.nih.gov/nuccore/NM_001195248) |
| dbSNP | [rs1563961179](https://www.ncbi.nlm.nih.gov/snp/rs1563961179/) |
| Variant type | Deletion |
| Location | chr9:32984806-32984813 (GRCh38) |
| ClinVar | [VCV2019865](https://www.ncbi.nlm.nih.gov/clinvar/variation/2019865/) |

**All HGVS expressions:** `NC_000009.11:g.32984807_32984814del`, `NC_000009.12:g.32984809_32984816del`, `NG_012821.2:g.45319_45326del`, `NM_001195248.2:c.588_595del`, `NM_001195249.2:c.588_595del`, `NM_001195250.2:c.426_433del`, `NM_001195251.2:c.588_595del`, `NM_001195252.2:c.372_379del`, `NM_001195254.2:c.426_433del`, `NM_001368995.1:c.588_595del`, `NM_001368996.1:c.588_595del`, `NM_001368997.1:c.588_595del`, `NM_001368998.1:c.588_595del`, `NM_001368999.1:c.588_595del`, `NM_001369000.1:c.426_433del`, `NM_001369001.1:c.426_433del`, `NM_001369002.1:c.324_331del`, `NM_001369003.1:c.324_331del`, `NM_001369004.1:c.324_331del`, `NM_001369005.1:c.324_331del`, `NM_001369006.1:c.324_331del`, `NM_001370669.1:c.324_331del`, `NM_001370670.1:c.324_331del`, `NM_001370673.1:c.324_331del`, `NM_175069.3:c.588_595del`, `NM_175071.1:c.63_70delCCCAAAGG`, `NM_175073.3:c.588_595del`, `NR_036576.1:n.659_666delCCCAAAGG`, `NR_036577.2:n.539_546del`, `NR_036578.1:n.681_688delCCCAAAGG`, `NR_036579.1:n.828_835delCCCAAAGG`, `NR_160921.1:n.558_565del`, `NR_160922.1:n.789_796del`, `NR_160923.1:n.593_600del`, `NR_160924.1:n.598_605del`, `NR_160925.1:n.794_801del`, `NR_160926.1:n.584_591del`, `NR_160930.1:n.534_541del`, `NR_160931.1:n.773_780del`

## 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 2.684, GERP 0.799, phastCons 0.999 — 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 6 of 8**, so the transcript is predicted to undergo NMD.
- CADD: **PHRED 35.0**. 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** — the release is built from a substitutions-only source, so it holds no deletion variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.00134%** (afr) · 1/74,906 in the highest group · 1/152,158 alleles overall — very rare (popmax 0.00134%, afr).

*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 **197** lies in the hit domain; 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.Lys197fs falls in the hit 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 2022-11-29.

**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 | 2022-11-29 |

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

## Similar variants {#similar}

Related APTX variant pages (same residue, condition, or type): [APTX p.Arg199fs](/variant/aptx-p-arg199fs), [APTX p.Val259fs](/variant/aptx-p-val259fs), [APTX c.484-13del](/variant/aptx-c-484-minus-13del), [APTX c.484-15_484-3del](/variant/aptx-c-484-minus-15-484-minus-3del), [APTX c.484-25_484-3del](/variant/aptx-c-484-minus-25-484-minus-3del), [APTX c.484-25_484-4del](/variant/aptx-c-484-minus-25-484-minus-4del), [APTX c.484-25_484-5del](/variant/aptx-c-484-minus-25-484-minus-5del), [APTX c.484-25_484-6del](/variant/aptx-c-484-minus-25-484-minus-6del).

### 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 2019865). 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.*