# NM_001195248.2(APTX):c.159G>A (p.Lys53=)

https://sugi.bio/variant/aptx-p-lys53

## Summary

**APTX p.Lys53= (c.159G>A)** is classified **Likely benign** in APTX (ClinVar, Single submitter, 1 submitter; last evaluated 2022-02-11). Very rare (popmax 8.47e-05%, nfe).

**At a glance:** Likely benign · review: Single submitter · rsID rs1207705618 · 1 submitter · very rare (popmax 8.47e-05%, nfe)

## For patients & families {#patients}

This is a change in the APTX gene that is classified as likely benign — not considered disease-causing, 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.Lys53= |
| Coding change (HGVS c.) | c.159G>A |
| MANE Select transcript | [NM_001195248](https://www.ncbi.nlm.nih.gov/nuccore/NM_001195248) |
| dbSNP | [rs1207705618](https://www.ncbi.nlm.nih.gov/snp/rs1207705618/) |
| Variant type | single nucleotide variant |
| Location | chr9:32988104-32988104 (GRCh38) |
| ClinVar | [VCV2095561](https://www.ncbi.nlm.nih.gov/clinvar/variation/2095561/) |

**All HGVS expressions:** `NC_000009.11:g.32988102C>T`, `NC_000009.12:g.32988104C>T`, `NG_012821.2:g.42028G>A`, `NM_001195248.2:c.159G>A`, `NM_001195249.2:c.159G>A`, `NM_001195250.2:c.134-373G>A`, `NM_001195251.2:c.159G>A`, `NM_001195252.2:c.159G>A`, `NM_001195254.2:c.134-373G>A`, `NM_001368995.1:c.159G>A`, `NM_001368996.1:c.159G>A`, `NM_001368997.1:c.159G>A`, `NM_001368998.1:c.159G>A`, `NM_001368999.1:c.159G>A`, `NM_001369000.1:c.134-373G>A`, `NM_001369001.1:c.134-373G>A`, `NM_001369002.1:c.-106G>A`, `NM_001369003.1:c.-106G>A`, `NM_001369004.1:c.-84-258G>A`, `NM_001369005.1:c.-106G>A`, `NM_001369006.1:c.-106G>A`, `NM_001370669.1:c.-106G>A`, `NM_001370670.1:c.-106G>A`, `NM_001370673.1:c.-106G>A`, `NM_175069.3:c.159G>A`, `NM_175071.1:c.-249G>A`, `NM_175073.3:c.159G>A`, `NR_036576.1:n.233G>A`, `NR_036577.2:n.225G>A`, `NR_036578.1:n.255G>A`, `NR_036579.1:n.402G>A`, `NR_160920.1:n.225G>A`, `NR_160921.1:n.244G>A`, `NR_160922.1:n.475G>A`, `NR_160923.1:n.279G>A`, `NR_160924.1:n.284G>A`, `NR_160925.1:n.480G>A`, `NR_160926.1:n.279G>A`, `NR_160927.1:n.475G>A`, `NR_160928.1:n.480G>A`, `NR_160929.1:n.279G>A`, `NR_160930.1:n.220G>A`, `NR_160931.1:n.459G>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 0.612, GERP -2.56, phastCons 0.998 — weakly conserved position
- CADD: **PHRED 9.65**. 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: **below the reporting threshold**. This position is scored for a different substitution (C>G, Δ0.25 donor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **8.47e-05%** (nfe) · 1/1,179,976 in the highest group · 1/1,614,120 alleles overall — very rare (popmax 8.47e-05%, nfe).

*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 **53** lies in the fha-like domain; the 'interactions with adprt/parp1 and ncl' region.

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.Lys53= 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}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-02-11.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2022-02-11 |

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

## Similar variants {#similar}

Related APTX variant pages (same residue, condition, or type): [APTX c.875-2A>G](/variant/aptx-c-875-minus-2a-g), [APTX p.Ala198Val](/variant/aptx-p-ala198val), [APTX p.Arg16Ter](/variant/aptx-p-arg16ter), [APTX p.Arg247Ter](/variant/aptx-p-arg247ter), [APTX p.Gln130Ter](/variant/aptx-p-gln130ter), [APTX p.Gln187Ter](/variant/aptx-p-gln187ter), [APTX p.Trp279Arg](/variant/aptx-p-trp279arg), [APTX p.Trp279Ter](/variant/aptx-p-trp279ter).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 2095561). 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.*