# NM_001725.3(BPI):c.534G>C (p.Val178=)

https://sugi.bio/variant/bpi-p-val178

## Summary

**BPI p.Val178= (c.534G>C)** is classified **Benign** in BPI (ClinVar, Multiple submitters, 2 submitters; last evaluated 2016-03-28). Common (popmax 14.3%, amr) — too common for a highly-penetrant pathogenic allele.

**At a glance:** Benign · review: Multiple submitters · rsID rs5743507 · 2 submitters · common (popmax 14.3%, amr) — too common for a highly-penetrant pathogenic allele

## For patients & families {#patients}

This is a change in the BPI gene that is classified as benign — not considered disease-causing, submitted by 2 submitters.

*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 | [BPI](https://sugi.bio/atlas/gene/BPI/) |
| Protein change (HGVS p.) | p.Val178= |
| Coding change (HGVS c.) | c.534G>C |
| MANE Select transcript | [NM_001725](https://www.ncbi.nlm.nih.gov/nuccore/NM_001725) |
| dbSNP | [rs5743507](https://www.ncbi.nlm.nih.gov/snp/rs5743507/) |
| Variant type | single nucleotide variant |
| Location | chr20:38310650-38310650 (GRCh38) |
| ClinVar | [VCV402432](https://www.ncbi.nlm.nih.gov/clinvar/variation/402432/) |

**All HGVS expressions:** `NC_000020.10:g.36939052G>C`, `NC_000020.11:g.38310650G>C`, `NG_047016.1:g.11501G>C`, `NM_001725.3:c.534G>C`

## Computational & population evidence {#evidence}

**Concordance:** Evidence sources **disagree** — common (popmax 14.3%, amr) — too common for a highly-penetrant pathogenic allele.

- **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 (below), not from a missing predictor score.
- Conservation: phyloP 0.666, GERP -0.18, phastCons 0.997 — weakly conserved position
- CADD: **PHRED 3.072**. 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: **below the reporting threshold**. This position is scored for a different substitution (G>A, Δ0.52 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 **14.3%** (amr) · FAF95 14% · FAF99 13.9% · 8,543/59,910 in the highest group · 167,468/1,611,708 alleles overall — common (popmax 14.3%, amr) — too common for a highly-penetrant pathogenic allele.

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Amish (not grpmax-eligible) | 24.6% | 4 |
| Admixed American (grpmax) | 14.3% | 7 |
| European (non-Finnish) | 11.6% | 9 |
| Finnish (not grpmax-eligible) | 10.5% | 10 |
| Ashkenazi Jewish (not grpmax-eligible) | 9.14% | 11 |
| Remaining individuals (not grpmax-eligible) | 9.08% | 11 |
| South Asian | 5.15% | 19 |
| Middle Eastern | 4.85% | 21 |
| African / African-American | 1.94% | 52 |
| East Asian | 0.029% | 3,446 |

Amish shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*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}

**BPI** population constraint: LOEUF 1.011, pLI 1.4953e-13, missense-Z -0.17135. *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 **178** lies in the 'n-terminal barrel' region.

AlphaFold model confidence (whole protein): pLDDT 92.70, 89% of residues very-high.

**2 experimental structure(s)** (PDB): [1BP1](https://www.rcsb.org/structure/1BP1), [1EWF](https://www.rcsb.org/structure/1EWF).

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

*Describes the biological roles of BPI (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:** BPI's established molecular role includes lipopolysaccharide binding. p.Val178= falls in the n-terminal barrel region.


### Pathways affected {#pathways}

BPI participates in **3 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Antimicrobial peptides](https://reactome.org/content/detail/R-HSA-6803157) | curated |
| [Neutrophil degranulation](https://reactome.org/content/detail/R-HSA-6798695) | curated |
| [Toll Like Receptor 4 (TLR4) Cascade](https://reactome.org/content/detail/R-HSA-166016) | curated |

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

**Molecular function:** lipopolysaccharide binding.

**Biological process:** negative regulation of interleukin-6 production, negative regulation of interleukin-8 production, negative regulation of tumor necrosis factor production, negative regulation of macrophage activation.

## Clinical significance {#significance}

**Benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2016-03-28.

**Submitter consensus:** unanimous (2/2 Benign).

**Submission history:** 2 submissions (2016); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Benign | criteria provided, single submitter | clinical testing | 2016-03-28 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |

**Reported phenotype names (ClinVar):** not specified, not provided, none provided, RECLASSIFIED - ADRA2C POLYMORPHISM, RECLASSIFIED - ADRB1 POLYMORPHISM, AllHighlyPenetrant.

## Similar variants {#similar}

Related BPI variant pages (same residue, condition, or type): [BPI c.664+7G>T](/variant/bpi-c-664-plus-7g-t), [BPI p.Ala12Val](/variant/bpi-p-ala12val), [BPI p.Ala192Val](/variant/bpi-p-ala192val), [BPI p.Ala333Thr](/variant/bpi-p-ala333thr), [BPI p.Ala8Thr](/variant/bpi-p-ala8thr), [BPI p.Ala8Val](/variant/bpi-p-ala8val), [BPI p.Arg86Cys](/variant/bpi-p-arg86cys), [BPI p.Glu136Gln](/variant/bpi-p-glu136gln).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 402432). 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.*