# NM_031885.5(BBS2):c.15_16del (p.Phe6fs)

https://sugi.bio/variant/bbs2-p-phe6fs

## Summary

**BBS2 p.Phe6fs (c.15_16del)** is classified **Likely pathogenic** in BBS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-24). Associated with BBS2-related disorder.

**At a glance:** Likely pathogenic · review: Single submitter · 1 submitter · 1 linked condition

## For patients & families {#patients}

This is a change in the BBS2 gene that is considered likely disease-causing, submitted by 1 submitter, and is linked to BBS2-related disorder.

*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 | [BBS2](https://sugi.bio/atlas/gene/BBS2/) |
| Protein change (HGVS p.) | p.Phe6fs |
| Coding change (HGVS c.) | c.15_16del |
| MANE Select transcript | [NM_031885](https://www.ncbi.nlm.nih.gov/nuccore/NM_031885) |
| Variant type | Microsatellite |
| Location | chr16:56519847-56519848 (GRCh38) |
| ClinVar | [VCV4930080](https://www.ncbi.nlm.nih.gov/clinvar/variation/4930080/) |

**All HGVS expressions:** `NC_000016.10:g.56519848CA[1]`, `NC_000016.9:g.56553760CA[1]`, `NG_009312.2:g.5175GT[1]`, `NM_001377456.1:c.15_16del`, `NM_031885.5:c.15_16del`, `NR_165293.1:n.175GT[1]`, `NR_165294.1:n.175GT[1]`, `NR_165295.1:n.175GT[1]`, `NR_165296.1:n.175GT[1]`, `NR_165297.1:n.175GT[1]`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- **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 11.031, GERP 2.04, phastCons 1 — highly conserved position (PP3-type support)
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 0.892, pLI 6.2071e-15. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 1 of 17**, so the transcript is predicted to undergo NMD.
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no microsatellite variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.

*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}

**BBS2** population constraint: LOEUF 0.892, pLI 6.2071e-15, missense-Z 1.9805. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **BBS2-related ciliopathy** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 89.49, 68% of residues very-high.

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

*Describes the biological roles of BBS2 (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:** BBS2's established molecular role includes RNA polymerase II-specific DNA-binding transcription factor binding.


### Pathways affected {#pathways}

BBS2 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [BBSome-mediated cargo-targeting to cilium](https://reactome.org/content/detail/R-HSA-5620922) | other |

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

**Molecular function:** RNA polymerase II-specific DNA-binding transcription factor binding.

**Biological process:** visual perception, Golgi to plasma membrane protein transport.

## Clinical significance {#significance}

**Likely pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2021-05-24.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Blueprint Genetics | Likely pathogenic | criteria provided, single submitter | clinical testing | 2021-05-24 |

## Associated conditions {#conditions}

[BBS2-related disorder](https://sugi.bio/atlas/disease/bbs2-related-disorder/).

**Reported phenotype names (ClinVar):** BBS2-related disorder, BBS2-related condition, BBS2-related disorders.

## Similar variants {#similar}

Related BBS2 variant pages (same residue, condition, or type): [BBS2 c.804+1_804+14del](/variant/bbs2-c-804-plus-1-804-plus-14del), [BBS2 c.941-1G>T](/variant/bbs2-c-941-minus-1g-t), [BBS2 p.Arg216Pro](/variant/bbs2-p-arg216pro), [BBS2 p.Arg234Ter](/variant/bbs2-p-arg234ter), [BBS2 p.Arg275Ter](/variant/bbs2-p-arg275ter), [BBS2 p.Arg703Ter](/variant/bbs2-p-arg703ter), [BBS2 p.Asn663Ter](/variant/bbs2-p-asn663ter), [BBS2 p.Asp104Ala](/variant/bbs2-p-asp104ala).

### 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 4930080). 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.*