# NM_057176.3(BSND):c.189C>T (p.Val63=)

https://sugi.bio/variant/bsnd-p-val63

## Summary

**BSND p.Val63= (c.189C>T)** is classified **Benign/Likely benign** in BSND (ClinVar, Multiple submitters, 13 submitters; last evaluated 2026-01-27). Rare (popmax 0.957%, mid); Associated with Bartter disease type 4A.

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs144505461 · 13 submitters · 2 linked conditions · rare (popmax 0.957%, mid)

## For patients & families {#patients}

This is a change in the BSND gene that is classified as benign/likely benign — not considered disease-causing, submitted by 13 submitters, and is linked to Bartter disease type 4A.

*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:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0015348/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [BSND](https://sugi.bio/atlas/gene/BSND/) |
| Protein change (HGVS p.) | p.Val63= |
| Coding change (HGVS c.) | c.189C>T |
| MANE Select transcript | [NM_057176](https://www.ncbi.nlm.nih.gov/nuccore/NM_057176) |
| dbSNP | [rs144505461](https://www.ncbi.nlm.nih.gov/snp/rs144505461/) |
| Variant type | single nucleotide variant |
| Location | chr1:55005033-55005033 (GRCh38) |
| ClinVar | [VCV46549](https://www.ncbi.nlm.nih.gov/clinvar/variation/46549/) |

**All HGVS expressions:** `LRG_1282:g.11101C>T`, `LRG_1282t1:c.189C>T`, `NC_000001.10:g.55470706C>T`, `NC_000001.11:g.55005033C>T`, `NG_008965.2:g.11101C>T`, `NM_057176.3:c.189C>T`

## 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 (below), not from a missing predictor score.
- Conservation: phyloP -0.349, GERP -2.45, phastCons 0.006 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 0.148**. 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: **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 **0.957%** (mid) · FAF95 0.76% · FAF99 0.689% · 58/6,062 in the highest group · 3,219/1,614,204 alleles overall — rare (popmax 0.957%, mid).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Middle Eastern (grpmax) | 0.957% | 105 |
| South Asian | 0.748% | 134 |
| Ashkenazi Jewish (not grpmax-eligible) | 0.564% | 177 |
| Admixed American | 0.273% | 366 |
| Remaining individuals (not grpmax-eligible) | 0.27% | 370 |
| European (non-Finnish) | 0.165% | 605 |
| African / African-American | 0.0293% | 3,412 |
| Finnish (not grpmax-eligible) | 0.00937% | 10,671 |
| East Asian | 0.00223% | 44,888 |

*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}

**BSND** population constraint: LOEUF 1.03, pLI 0.00065519, missense-Z 1.0448; ClinGen dosage — haploinsufficiency 30, triplosensitivity 0 (0–3 scale). *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):

- **Bartter disease type 4A** — Definitive (AR)

## Protein context {#protein}

Residue **63** lies in a UniProt-annotated variant site (in barts4a); a UniProt-annotated variant site (in barts4a; loss of clcnka and clcnkb channel conductance); the 'regulates channel membrane trafficking and ion conductance' region.

AlphaFold model confidence (whole protein): pLDDT 53.80, 0% of residues very-high.

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

*Describes the biological roles of BSND (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:** BSND's established molecular role includes chloride channel regulator activity. p.Val63= falls in the regulates channel membrane trafficking and ion conductance region.


### Pathways affected {#pathways}

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

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Stimuli-sensing channels](https://reactome.org/content/detail/R-HSA-2672351) | curated |

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

**Molecular function:** chloride channel regulator activity.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2026-01-27.

**Submitter consensus:** conflicting (7 Likely benign, 6 Benign).

**Submission history:** 13 submissions (2015–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Natera, Inc. | Likely benign | no assertion criteria provided | clinical testing | 2019-10-22 |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2018-05-29 |
| Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Benign | criteria provided, single submitter | clinical testing | 2015-07-01 |
| Genome Diagnostics Laboratory, University Medical Center Utrecht | Likely benign | no assertion criteria provided | clinical testing |  |
| Eurofins Ntd Llc (ga) | Benign | criteria provided, single submitter | clinical testing | 2016-09-09 |
| Genome-Nilou Lab | Benign | criteria provided, single submitter | clinical testing | 2021-06-10 |
| Mayo Clinic Laboratories, Mayo Clinic | Benign | criteria provided, single submitter | clinical testing | 2023-06-09 |
| CeGaT Center for Human Genetics Tuebingen | Likely benign | criteria provided, single submitter | clinical testing | 2023-01-01 |
| Illumina Laboratory Services, Illumina | Likely benign | criteria provided, single submitter | clinical testing | 2018-01-13 |
| Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Likely benign | no assertion criteria provided | clinical testing |  |
| Breakthrough Genomics, Breakthrough Genomics | Likely benign | criteria provided, single submitter | not provided |  |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-01-27 |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-11-21 |

## Associated conditions {#conditions}

[Bartter disease type 4A](https://sugi.bio/atlas/disease/bartter-disease-type-4a/), [Bartter syndrome](https://sugi.bio/atlas/disease/bartter-syndrome/).

**Reported phenotype names (ClinVar):** Bartter disease type 4A, not specified, not provided, Bartter syndrome, AllHighlyPenetrant, none provided, BARTTER SYNDROME, TYPE 4A, NEONATAL, WITH SENSORINEURAL DEAFNESS, BARTTER SYNDROME, NEONATAL, WITH SENSORINEURAL DEAFNESS.

## Similar variants {#similar}

Related BSND variant pages (same residue, condition, or type): [BSND p.Val63Ile](/variant/bsnd-p-val63ile), [BSND c.178-2A>C](/variant/bsnd-c-178-minus-2a-c), [BSND c.272+1G>T](/variant/bsnd-c-272-plus-1g-t), [BSND p.Arg8Trp](/variant/bsnd-p-arg8trp), [BSND p.Gln95Ter](/variant/bsnd-p-gln95ter), [BSND p.Glu148Ter](/variant/bsnd-p-glu148ter), [BSND p.Glu4Ter](/variant/bsnd-p-glu4ter), [BSND p.Glu88Ter](/variant/bsnd-p-glu88ter).

### 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 46549). 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.*