# NM_001031689.3(PLAA):c.1203T>C (p.Phe401=)

https://sugi.bio/variant/plaa-p-phe401

## Summary

**PLAA p.Phe401= (c.1203T>C)** is classified **Likely benign** in PLAA (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-18). Very rare (popmax 0.00812%, afr).

**At a glance:** Likely benign · review: Single submitter · rsID rs892171621 · 1 submitter · very rare (popmax 0.00812%, afr)

## For patients & families {#patients}

This is a change in the PLAA 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 | [PLAA](https://sugi.bio/atlas/gene/PLAA/) |
| Protein change (HGVS p.) | p.Phe401= |
| Coding change (HGVS c.) | c.1203T>C |
| MANE Select transcript | [NM_001031689](https://www.ncbi.nlm.nih.gov/nuccore/NM_001031689) |
| dbSNP | [rs892171621](https://www.ncbi.nlm.nih.gov/snp/rs892171621/) |
| Variant type | single nucleotide variant |
| Location | chr9:26919524-26919524 (GRCh38) |
| ClinVar | [VCV1648474](https://www.ncbi.nlm.nih.gov/clinvar/variation/1648474/) |

**All HGVS expressions:** `NC_000009.11:g.26919522A>G`, `NC_000009.12:g.26919524A>G`, `NM_001031689.3:c.1203T>C`, `NM_001321546.2:c.1203T>C`

## 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 loss** (Δ 0.26) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP 7.102, GERP 0.477, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 9.681**. 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 **0.26**, donor loss **0.00**, acceptor gain **0.00**, donor gain **0.00**. Largest is acceptor loss, 32 bp away.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.00**, donor gain **0.00**.
  Masked SpliceAI — what Ensembl VEP and the Broad lookup serve by default — is below the reporting threshold here, so those tools show **no splice signal** for this allele. Masking zeroes a loss scored against a position that is not an annotated splice site, and a gain that merely strengthens an existing one, so the raw score above is describing a cryptic site rather than the site the variant sits on. *No ACMG code is assigned either way.*
- Population frequency (gnomAD v4.1): grpmax **0.00812%** (afr) · FAF95 0.00351% · FAF99 0.00241% · 6/73,890 in the highest group · 7/1,563,614 alleles overall — very rare (popmax 0.00812%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| African / African-American (grpmax) | 0.00812% | 12,315 |
| Remaining individuals (not grpmax-eligible) | 0.00165% | 60,786 |

*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}

**PLAA** population constraint: LOEUF 0.678, pLI 0.0023759, missense-Z 0.69065. *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 **401** lies in a β-strand; the pfu domain.

AlphaFold model confidence (whole protein): pLDDT 84.87, 58% of residues very-high.

**5 experimental structure(s)** (PDB): [2K89](https://www.rcsb.org/structure/2K89), [2K8A](https://www.rcsb.org/structure/2K8A), [2K8B](https://www.rcsb.org/structure/2K8B), [2K8C](https://www.rcsb.org/structure/2K8C), [3EBB](https://www.rcsb.org/structure/3EBB).

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

*Describes the biological roles of PLAA (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:** PLAA's established molecular role includes phospholipase A2 activator activity. p.Phe401= falls in the pfu domain.


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

**Molecular function:** phospholipase A2 activator activity.

**Biological process:** macroautophagy, cellular response to lipopolysaccharide.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-12-18.

**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 | 2023-12-18 |

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

## Similar variants {#similar}

Related PLAA variant pages (same residue, condition, or type): [PLAA p.Arg524Ter](/variant/plaa-p-arg524ter), [PLAA p.Ala156Val](/variant/plaa-p-ala156val), [PLAA p.Ala264Thr](/variant/plaa-p-ala264thr), [PLAA p.Ala271Val](/variant/plaa-p-ala271val), [PLAA p.Arg268Gln](/variant/plaa-p-arg268gln), [PLAA p.Arg373Thr](/variant/plaa-p-arg373thr), [PLAA p.Arg499Cys](/variant/plaa-p-arg499cys), [PLAA p.Arg7Ser](/variant/plaa-p-arg7ser).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); 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 2026-10-14); 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 1648474). 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.*