# NM_001142930.2(API5):c.1512G>A (p.Arg504=)

https://sugi.bio/variant/api5-p-arg504

## Summary

**API5 p.Arg504= (c.1512G>A)** is classified **Likely benign** in API5 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-17). Ultra-rare (popmax 0.016%, afr).

**At a glance:** Likely benign · review: Single submitter · rsID rs560522772 · 1 submitter · ultra-rare (popmax 0.016%, afr)

## For patients & families {#patients}

This is a change in the API5 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 | [API5](https://sugi.bio/atlas/gene/API5/) |
| Protein change (HGVS p.) | p.Arg504= |
| Coding change (HGVS c.) | c.1512G>A |
| MANE Select transcript | [NM_001142930](https://www.ncbi.nlm.nih.gov/nuccore/NM_001142930) |
| dbSNP | [rs560522772](https://www.ncbi.nlm.nih.gov/snp/rs560522772/) |
| Variant type | single nucleotide variant |
| Location | chr11:43342447-43342447 (GRCh38) |
| ClinVar | [VCV3127820](https://www.ncbi.nlm.nih.gov/clinvar/variation/3127820/) |

**All HGVS expressions:** `NC_000011.10:g.43342447G>A`, `NC_000011.9:g.43363997G>A`, `NG_029841.2:g.35453G>A`, `NM_001142930.2:c.1512G>A`, `NM_001142931.2:c.1345G>A`, `NM_001243747.2:c.988G>A`, `NM_006595.4:c.1507G>A`, `NR_024625.2:n.1706G>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 and, for splice-region changes, SpliceAI (below), not from a missing predictor score.
- SpliceAI predicts **acceptor gain** (Δ 0.29) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP 11.869, GERP 1.92, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 12.78**. 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 deltas (raw): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.29**, donor gain **0.00**. Largest is acceptor gain.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.29**, donor gain **0.00**.
- Population frequency (gnomAD v4.1): grpmax **0.016%** (afr) · FAF95 0.00921% · FAF99 0.00721% · 12/74,950 in the highest group · 13/1,610,680 alleles overall — ultra-rare (popmax 0.016%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.016% | 6,246 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,328 |

*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}

**API5** population constraint: LOEUF 0.211, pLI 1, missense-Z 3.6846. *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 **504** lies in the 'disordered' region.

AlphaFold model confidence (whole protein): pLDDT 85.04, 76% of residues very-high.

**3 experimental structure(s)** (PDB): [3U0R](https://www.rcsb.org/structure/3U0R), [3V6A](https://www.rcsb.org/structure/3V6A), [6L4O](https://www.rcsb.org/structure/6L4O).

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

*Describes the biological roles of API5 (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:** API5's established molecular role includes RNA binding. p.Arg504= falls in the disordered region.


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

**Molecular function:** RNA binding, fibroblast growth factor binding.

**Biological process:** negative regulation of apoptotic process.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-10-17.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2023-10-17 |

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

## Similar variants {#similar}

Related API5 variant pages (same residue, condition, or type): [API5 p.Ala402Thr](/variant/api5-p-ala402thr), [API5 p.Arg243Trp](/variant/api5-p-arg243trp), [API5 p.Asn517His](/variant/api5-p-asn517his), [API5 p.Asp164Glu](/variant/api5-p-asp164glu), [API5 p.Asp359His](/variant/api5-p-asp359his), [API5 p.Asp427His](/variant/api5-p-asp427his), [API5 p.Cys234Tyr](/variant/api5-p-cys234tyr), [API5 p.Glu215Gln](/variant/api5-p-glu215gln).

### 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 3127820). 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.*