# NM_020531.3(APMAP):c.410C>T (p.Ser137Leu)

https://sugi.bio/variant/apmap-p-ser137leu

## Summary

**APMAP p.Ser137Leu (c.410C>T)** is classified **Uncertain significance** in APMAP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-11). AlphaMissense: likely benign (0.0908); Ultra-rare (popmax 0.0379%, eas).

**At a glance:** Uncertain significance · review: Single submitter · rsID rs371061783 · 1 submitter · AlphaMissense likely benign · ultra-rare (popmax 0.0379%, eas)

## For patients & families {#patients}

This is a change in the APMAP 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 | [APMAP](https://sugi.bio/atlas/gene/APMAP/) |
| Protein change (HGVS p.) | p.Ser137Leu |
| Coding change (HGVS c.) | c.410C>T |
| MANE Select transcript | [NM_020531](https://www.ncbi.nlm.nih.gov/nuccore/NM_020531) |
| dbSNP | [rs371061783](https://www.ncbi.nlm.nih.gov/snp/rs371061783/) |
| Variant type | single nucleotide variant |
| Location | chr20:24973656-24973656 (GRCh38) |
| ClinVar | [VCV2470140](https://www.ncbi.nlm.nih.gov/clinvar/variation/2470140/) |

**All HGVS expressions:** `NC_000020.10:g.24954292G>A`, `NC_000020.11:g.24973656G>A`, `NM_020531.3:c.410C>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely benign** (0.0908)
- REVEL 0.15 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -8.44 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 7.052, GERP 1.42, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 23.2**. 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 0.92** across the covering region of the MANE Select transcript (24,963,816–24,992,688), spanning 28,872 bp. Chi-square p 0.066. 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 (G>T, Δ0.41 donor loss), 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 **0.0379%** (eas) · FAF95 0.0241% · FAF99 0.0197% · 17/44,880 in the highest group · 96/1,613,912 alleles overall — ultra-rare (popmax 0.0379%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.0379% | 2,640 |
| African / African-American | 0.0227% | 4,414 |
| Remaining individuals (not grpmax-eligible) | 0.008% | 12,498 |
| South Asian | 0.00549% | 18,213 |
| European (non-Finnish) | 0.00432% | 23,134 |
| Admixed American | 0.00167% | 60,008 |

*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}

**APMAP** population constraint: LOEUF 1.14, pLI 2.4673e-10, missense-Z 0.79561. *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 91.60, 84% of residues very-high.

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

*Describes the biological roles of APMAP (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:** APMAP's established molecular role includes arylesterase activity.


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

**Molecular function:** arylesterase activity.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-12-11.

**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 | 2025-12-11 |

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

## Similar variants {#similar}

Related APMAP variant pages (same residue, condition, or type): [APMAP p.Ala47Gly](/variant/apmap-p-ala47gly), [APMAP p.Arg120Trp](/variant/apmap-p-arg120trp), [APMAP p.Arg134Gln](/variant/apmap-p-arg134gln), [APMAP p.Arg134Pro](/variant/apmap-p-arg134pro), [APMAP p.Arg143Gly](/variant/apmap-p-arg143gly), [APMAP p.Arg156Cys](/variant/apmap-p-arg156cys), [APMAP p.Arg156His](/variant/apmap-p-arg156his), [APMAP p.Arg224Gln](/variant/apmap-p-arg224gln).

### 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 2470140). 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.*