# NM_001170795.4(ATRAID):c.35T>C (p.Leu12Pro)

https://sugi.bio/variant/atraid-p-leu12pro

## Summary

**ATRAID p.Leu12Pro (c.35T>C)** is classified **Uncertain significance** in ATRAID (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-13). AlphaMissense: likely benign (0.047); Very rare (popmax 0.00137%, afr).

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter · AlphaMissense likely benign · very rare (popmax 0.00137%, afr)

## For patients & families {#patients}

This is a change in the ATRAID 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 | [ATRAID](https://sugi.bio/atlas/gene/ATRAID/) |
| Protein change (HGVS p.) | p.Leu12Pro |
| Coding change (HGVS c.) | c.35T>C |
| MANE Select transcript | [NM_001170795](https://www.ncbi.nlm.nih.gov/nuccore/NM_001170795) |
| Variant type | single nucleotide variant |
| Location | chr2:27212403-27212403 (GRCh38) |
| ClinVar | [VCV3975345](https://www.ncbi.nlm.nih.gov/clinvar/variation/3975345/) |

**All HGVS expressions:** `NC_000002.11:g.27435271T>C`, `NC_000002.12:g.27212403T>C`, `NG_046394.1:g.14T>C`, `NG_166390.1:g.289T>C`, `NM_001170795.4:c.35T>C`, `NM_016085.5:c.-280T>C`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.047)
- REVEL 0.038 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -7.609 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 0.107, GERP -4.74 — weakly conserved position
- CADD: **PHRED 8.557**. 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 1.08** across the covering region of the MANE Select transcript (27,212,369–27,216,945), spanning 4,576 bp. Chi-square p 0.19. 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 (T>A, Δ0.40 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 **0.00137%** (afr) · FAF95 8.2e-05% · FAF99 5.5e-05% · 1/72,974 in the highest group · 5/1,551,804 alleles overall — very rare (popmax 0.00137%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.00137% | 72,974 |
| European (non-Finnish) | 0.000348% | 286,950 |

*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}

**ATRAID** population constraint: LOEUF 1.235, pLI 1.0538e-08, missense-Z -0.40297. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 87.31, 70% of residues very-high.

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

*Describes the biological roles of ATRAID (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:** ATRAID's established molecular role includes xenobiotic transmembrane transporter activity.


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

**Molecular function:** xenobiotic transmembrane transporter activity.

**Biological process:** xenobiotic transmembrane transport, regulation of gene expression, positive regulation of bone mineralization, negative regulation of osteoblast proliferation, negative regulation of protein catabolic process, positive regulation of osteoblast differentiation.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-05-13.

**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 | 2025-05-13 |

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

## Similar variants {#similar}

Related ATRAID variant pages (same residue, condition, or type): [ATRAID p.Leu12Val](/variant/atraid-p-leu12val), [ATRAID c.-117C>A](/variant/atraid-c-minus-117c-a), [ATRAID c.-123A>C](/variant/atraid-c-minus-123a-c), [ATRAID c.-155G>A](/variant/atraid-c-minus-155g-a), [ATRAID c.-161A>G](/variant/atraid-c-minus-161a-g), [ATRAID c.-24A>T](/variant/atraid-c-minus-24a-t), [ATRAID c.-38C>T](/variant/atraid-c-minus-38c-t), [ATRAID c.-44C>G](/variant/atraid-c-minus-44c-g).

### 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 3975345). 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.*