# NM_001171.6(ABCC6):c.2047del (p.Val683fs)

https://sugi.bio/variant/abcc6-p-val683fs

## Summary

**ABCC6 p.Val683fs (c.2047del)** is classified **Pathogenic** in ABCC6 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-05). Very rare (popmax 0.005%, amr).

**At a glance:** Pathogenic · review: Single submitter · 1 submitter · very rare (popmax 0.005%, amr)

## For patients & families {#patients}

This is a change in the ABCC6 gene that is reported as disease-causing, but on limited review, 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 | [ABCC6](https://sugi.bio/atlas/gene/ABCC6/) |
| Protein change (HGVS p.) | p.Val683fs |
| Coding change (HGVS c.) | c.2047del |
| MANE Select transcript | [NM_001171](https://www.ncbi.nlm.nih.gov/nuccore/NM_001171) |
| Variant type | Deletion |
| Location | chr16:16182827-16182827 (GRCh38) |
| ClinVar | [VCV3675870](https://www.ncbi.nlm.nih.gov/clinvar/variation/3675870/) |

**All HGVS expressions:** `LRG_1115:g.45791del`, `LRG_1115t1:c.2047del`, `NC_000016.10:g.16182828del`, `NC_000016.9:g.16276685del`, `NG_007558.3:g.45791del`, `NM_001171.6:c.2047del`, `NM_001351800.1:c.1705del`, `NR_147784.1:n.2084del`

## 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 7.905, GERP 1.84, phastCons 0.998 — highly conserved position (PP3-type support)
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 0.917, pLI 1.2351e-33. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 16 of 31**, so the transcript is predicted to undergo NMD.
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no deletion variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **0.005%** (amr) · FAF95 0.00133% · FAF99 0.000668% · 3/60,000 in the highest group · 3/1,461,834 alleles overall — very rare (popmax 0.005%, amr).

*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}

**ABCC6** population constraint: LOEUF 0.917, pLI 1.2351e-33, missense-Z 1.031. *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):

- **inherited pseudoxanthoma elasticum** — Definitive (SD)

## Protein context {#protein}

Residue **683** lies in a β-strand; the abc transporter 1 domain.

AlphaFold model confidence (whole protein): pLDDT 81.32, 29% of residues very-high.

**4 experimental structure(s)** (PDB): [6BZR](https://www.rcsb.org/structure/6BZR), [6BZS](https://www.rcsb.org/structure/6BZS), [6NLO](https://www.rcsb.org/structure/6NLO), [6P7F](https://www.rcsb.org/structure/6P7F) — incl. mutant structure 6P7F.

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

*Describes the biological roles of ABCC6 (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:** ABCC6's established molecular role includes ATP binding. p.Val683fs falls in the abc transporter 1 domain. In Reactome, ABCC6 is annotated in disease pathway(s) including **Defective ABCC6 causes PXE**.

**Disease mechanism (Reactome):** ABCC6 loss or alteration is curated in [Defective ABCC6 causes PXE](https://reactome.org/content/detail/R-HSA-5690338).

### Pathways affected {#pathways}

ABCC6 participates in **2 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective ABCC6 causes PXE](https://reactome.org/content/detail/R-HSA-5690338) | curated |
| [ABC-family protein mediated transport](https://reactome.org/content/detail/R-HSA-382556) | curated |

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

**Molecular function:** ATP binding, ABC-type glutathione S-conjugate transporter activity, ATPase-coupled transmembrane transporter activity.

**Biological process:** gene expression, ATP transport, ATP metabolic process, phosphate ion homeostasis, calcium ion homeostasis, leukotriene transport.

## Clinical significance {#significance}

**Pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2025-03-05.

**Submitter consensus:** unanimous (1/1 Pathogenic).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2025-03-05 |

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

## Similar variants {#similar}

Related ABCC6 variant pages (same residue, condition, or type): [ABCC6 p.Val683=](/variant/abcc6-p-val683), [ABCC6 c.2248-2_2248-1del](/variant/abcc6-c-2248-minus-2-2248-minus-1del), [ABCC6 c.3506+2_3506+5del](/variant/abcc6-c-3506-plus-2-3506-plus-5del), [ABCC6 c.998+2_998+3del](/variant/abcc6-c-998-plus-2-998-plus-3del), [ABCC6 p.Ala667fs](/variant/abcc6-p-ala667fs), [ABCC6 p.Arg473fs](/variant/abcc6-p-arg473fs), [ABCC6 p.Asp1368fs](/variant/abcc6-p-asp1368fs), [ABCC6 p.Glu559fs](/variant/abcc6-p-glu559fs).

### 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 3675870). 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.*