# NM_130384.3(ATRIP):c.1673C>A (p.Ala558Asp)

https://sugi.bio/variant/atrip-p-ala558asp

## Summary

**ATRIP p.Ala558Asp (c.1673C>A)** is classified **Uncertain significance** in ATRIP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-03). AlphaMissense: likely benign (0.1234); Absent from gnomAD v4.1.

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter · AlphaMissense likely benign · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the ATRIP gene that is currently of uncertain significance — a definitive interpretation has not yet been established, 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 | [ATRIP](https://sugi.bio/atlas/gene/ATRIP/) |
| Protein change (HGVS p.) | p.Ala558Asp |
| Coding change (HGVS c.) | c.1673C>A |
| MANE Select transcript | [NM_130384](https://www.ncbi.nlm.nih.gov/nuccore/NM_130384) |
| Variant type | single nucleotide variant |
| Location | chr3:48460727-48460727 (GRCh38) |
| ClinVar | [VCV3810393](https://www.ncbi.nlm.nih.gov/clinvar/variation/3810393/) |

**All HGVS expressions:** `NC_000003.11:g.48502126C>A`, `NC_000003.12:g.48460727C>A`, `NG_041782.1:g.19018C>A`, `NM_001271022.2:c.1292C>A`, `NM_001271023.2:c.1394C>A`, `NM_032166.4:c.1673C>A`, `NM_130384.3:c.1673C>A`, `NR_153405.1:n.1740C>A`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.1234)
- REVEL 0.122 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -7.378 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 1.72, GERP -1.66, phastCons 0.979 — weakly conserved position
- CADD: **PHRED 19.43**. 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 0.95** across the covering region of the MANE Select transcript (48,446,846–48,465,551), spanning 18,705 bp. Chi-square p 0.089. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **below the reporting threshold**. This position is scored for a different substitution (C>T, Δ0.22 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: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*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}

**ATRIP** population constraint: LOEUF 0.707, pLI 1.4374e-06, missense-Z 0.4195. *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):

- **hereditary breast carcinoma** — Limited (AD)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 70.10, 35% of residues very-high.

**24 experimental structure(s)** (PDB): [4IGK](https://www.rcsb.org/structure/4IGK), [4NB3](https://www.rcsb.org/structure/4NB3), [5YZ0](https://www.rcsb.org/structure/5YZ0), [7XV4](https://www.rcsb.org/structure/7XV4), [13DE](https://www.rcsb.org/structure/13DE), [23EW](https://www.rcsb.org/structure/23EW).

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

*Describes the biological roles of ATRIP (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:** ATRIP's established molecular role includes K63-linked polyubiquitin modification-dependent protein binding. In Reactome, ATRIP is annotated in disease pathway(s) including **Impaired BRCA2 binding to RAD51**.

**Disease mechanism (Reactome):** ATRIP loss or alteration is curated in [Impaired BRCA2 binding to RAD51](https://reactome.org/content/detail/R-HSA-9709570).

### Pathways affected {#pathways}

ATRIP participates in **8 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Impaired BRCA2 binding to RAD51](https://reactome.org/content/detail/R-HSA-9709570) | curated |
| [Activation of ATR in response to replication stress](https://reactome.org/content/detail/R-HSA-176187) | curated |
| [Fanconi Anemia Pathway](https://reactome.org/content/detail/R-HSA-6783310) | curated |
| [G2/M DNA damage checkpoint](https://reactome.org/content/detail/R-HSA-69473) | curated |
| [HDR through Single Strand Annealing (SSA)](https://reactome.org/content/detail/R-HSA-5685938) | curated |
| [Presynaptic phase of homologous DNA pairing and strand exchange](https://reactome.org/content/detail/R-HSA-5693616) | curated |
| [Processing of DNA double-strand break ends](https://reactome.org/content/detail/R-HSA-5693607) | curated |
| [Regulation of TP53 Activity through Phosphorylation](https://reactome.org/content/detail/R-HSA-6804756) | curated |

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

**Molecular function:** K63-linked polyubiquitin modification-dependent protein binding.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-02-03.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-02-03 |

**Reported phenotype names (ClinVar):** not specified, AllHighlyPenetrant.

## Similar variants {#similar}

Related ATRIP variant pages (same residue, condition, or type): [ATRIP p.Ala558Gly](/variant/atrip-p-ala558gly), [TREX1 p.Arg114His](/variant/trex1-p-arg114his), [TREX1 p.Arg164Ter](/variant/trex1-p-arg164ter), [TREX1 p.Asp18Asn](/variant/trex1-p-asp18asn), [TREX1 p.Asp200His](/variant/trex1-p-asp200his), [TREX1 p.Gln135Ter](/variant/trex1-p-gln135ter), [ATRIP p.Ala119Thr](/variant/atrip-p-ala119thr), [ATRIP p.Ala173Val](/variant/atrip-p-ala173val).

### 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 3810393). 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.*