# NM_031885.5(BBS2):c.98C>A (p.Ala33Asp)

https://sugi.bio/variant/bbs2-p-ala33asp

## Summary

**BBS2 p.Ala33Asp (c.98C>A)** is classified **Conflicting classifications of pathogenicity** in BBS2 (ClinVar, Conflicting submitters, 8 submitters; last evaluated 2026-01-27). AlphaMissense: likely pathogenic (0.9902); Very rare (popmax 0.00167%, amr); Associated with BBS2-related disorder.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs797045155 · 8 submitters · 5 linked conditions · AlphaMissense likely pathogenic · very rare (popmax 0.00167%, amr)

## For patients & families {#patients}

This is a change in the BBS2 gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 8 submitters, 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.Ala33Asp |
| Coding change (HGVS c.) | c.98C>A |
| MANE Select transcript | [NM_031885](https://www.ncbi.nlm.nih.gov/nuccore/NM_031885) |
| dbSNP | [rs797045155](https://www.ncbi.nlm.nih.gov/snp/rs797045155/) |
| Variant type | single nucleotide variant |
| Location | chr16:56519765-56519765 (GRCh38) |
| ClinVar | [VCV209042](https://www.ncbi.nlm.nih.gov/clinvar/variation/209042/) |

**All HGVS expressions:** `NC_000016.10:g.56519765G>T`, `NC_000016.9:g.56553677G>T`, `NG_009312.2:g.5260C>A`, `NM_001377456.1:c.98C>A`, `NM_031885.5:c.98C>A`, `NR_165293.1:n.260C>A`, `NR_165294.1:n.260C>A`, `NR_165295.1:n.260C>A`, `NR_165296.1:n.260C>A`, `NR_165297.1:n.260C>A`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- AlphaMissense **likely pathogenic** (0.9902)
- REVEL 0.872 (moderately pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -12.378 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this damaging
- Conservation: phyloP 9.684, GERP 2.04, phastCons 1 — highly conserved (agrees)
- AlphaMissense ranks this among the **top 2%** most-pathogenic-predicted substitutions in BBS2 (of 4,272 modeled).
- CADD: **PHRED 33.0**. 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 0.87** across the covering region of the MANE Select transcript (56,484,764–56,519,862), spanning 35,098 bp. Chi-square p 9.6e-05. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.00167%** (amr) · FAF95 6.8e-05% · FAF99 1.9e-05% · 1/59,970 in the highest group · 5/1,613,096 alleles overall — very rare (popmax 0.00167%, amr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Admixed American (grpmax) | 0.00167% | 59,970 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,402 |
| European (non-Finnish) | 0.000254% | 393,165 |

*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}

Residue **33** lies in a UniProt-annotated variant site (in rp74).

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}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2026-01-27.

**Submitter consensus:** conflicting (3 Pathogenic, 3 Likely pathogenic, 2 Uncertain significance).

**Submission history:** 8 submissions (2015–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| OMIM | Pathogenic | no assertion criteria provided | literature only | 2015-03-01 |
| Laboratory of Medical Genetics, National & Kapodistrian University of Athens | Likely pathogenic | criteria provided, single submitter | clinical testing | 2021-10-01 |
| Myriad Genetics, Inc. | Uncertain significance | criteria provided, single submitter | clinical testing | 2021-11-15 |
| Natera, Inc. | Likely pathogenic | criteria provided, single submitter | clinical testing | 2025-09-17 |
| Sharon lab, Hadassah-Hebrew University Medical Center | Likely pathogenic | no assertion criteria provided | research | 2019-06-23 |
| PreventionGenetics, part of Exact Sciences | Uncertain significance | no assertion criteria provided | clinical testing | 2024-02-01 |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2026-01-27 |
| Blueprint Genetics | Pathogenic | criteria provided, single submitter | clinical testing | 2022-04-06 |

## Associated conditions {#conditions}

[BBS2-related disorder](https://sugi.bio/atlas/disease/bbs2-related-disorder/), [Bardet-Biedl syndrome 2](https://sugi.bio/atlas/disease/bardet-biedl-syndrome-2/), [retinitis pigmentosa 74](https://sugi.bio/atlas/disease/retinitis-pigmentosa-74/), [Bardet-Biedl syndrome](https://sugi.bio/atlas/disease/bardet-biedl-syndrome/), [retinitis pigmentosa](https://sugi.bio/atlas/disease/retinitis-pigmentosa/).

**Reported phenotype names (ClinVar):** BBS2-related disorder, Retinitis pigmentosa 74, Bardet-Biedl syndrome 2, Retinitis pigmentosa, Bardet-Biedl syndrome, BBS2-related condition, BBS2-related disorders.

## Similar variants {#similar}

Related BBS2 variant pages (same residue, condition, or type): [BBS2 p.Ala33=](/variant/bbs2-p-ala33), [BBS2 c.118-1G>T](/variant/bbs2-c-118-minus-1g-t), [BBS2 c.118-2A>C](/variant/bbs2-c-118-minus-2a-c), [BBS2 c.118-2A>G](/variant/bbs2-c-118-minus-2a-g), [BBS2 c.1225+2T>C](/variant/bbs2-c-1225-plus-2t-c), [BBS2 c.1225+2T>G](/variant/bbs2-c-1225-plus-2t-g), [BBS2 c.1397+1G>A](/variant/bbs2-c-1397-plus-1g-a), [BBS2 c.1397+2T>C](/variant/bbs2-c-1397-plus-2t-c).

### 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 209042). 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.*