# NM_000443.4(ABCB4):c.2306_2309del (p.Phe769fs)

https://sugi.bio/variant/abcb4-p-phe769fs

## Summary

**ABCB4 p.Phe769fs (c.2306_2309del)** is classified **Pathogenic** in ABCB4 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-01). No gnomAD frequency available for this variant; Associated with progressive familial intrahepatic cholestasis type 3.

**At a glance:** Pathogenic · review: Single submitter · rsID rs2546785095 · 1 submitter · 1 linked condition · no gnomAD frequency available for this variant

## For patients & families {#patients}

This is a change in the ABCB4 gene that is reported as disease-causing, but on limited review, submitted by 1 submitter, and is linked to progressive familial intrahepatic cholestasis type 3.

*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.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | Adolescent, Childhood, Infancy, Neonatal |
| Clinical trials | 1 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | ABCB4 is a diagnostic-grade gene on 8 Genomics England panels |

**Commonly reported features of Progressive familial intrahepatic cholestasis** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Jaundice — Very frequent (99-80%)
- Cholestasis — Very frequent (99-80%)
- Failure to thrive — Very frequent (99-80%)
- Splenomegaly — Very frequent (99-80%)
- Abnormality of coagulation — Very frequent (99-80%)
- Malabsorption — Very frequent (99-80%)
- Hepatomegaly — Very frequent (99-80%)
- Short stature — Very frequent (99-80%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0001289/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [ABCB4](https://sugi.bio/atlas/gene/ABCB4/) |
| Protein change (HGVS p.) | p.Phe769fs |
| Coding change (HGVS c.) | c.2306_2309del |
| MANE Select transcript | [NM_000443](https://www.ncbi.nlm.nih.gov/nuccore/NM_000443) |
| dbSNP | [rs2546785095](https://www.ncbi.nlm.nih.gov/snp/rs2546785095/) |
| Variant type | Deletion |
| Location | chr7:87422128-87422131 (GRCh38) |
| ClinVar | [VCV2687808](https://www.ncbi.nlm.nih.gov/clinvar/variation/2687808/) |

**All HGVS expressions:** `NC_000007.13:g.87051447_87051450del`, `NC_000007.14:g.87422131_87422134del`, `NG_007118.2:g.63302_63305del`, `NG_007118.3:g.58896_58899del`, `NM_000443.4:c.2306_2309del`, `NM_018849.3:c.2306_2309del`, `NM_018850.3:c.2306_2309del`

## 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 3.062, GERP 1.71, phastCons 1 — highly conserved position (PP3-type support)
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. ClinGen curates **sufficient evidence for haploinsufficiency** in this gene, supporting a loss-of-function disease mechanism. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 18 of 28**, 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: **no gnomAD frequency available for this variant** — rarity (ACMG PM2) and BA1/BS1 cannot be assessed for this variant.

*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}

**ABCB4** population constraint: LOEUF 0.623, pLI 1.7893e-08, missense-Z 3.5556; ClinGen dosage — haploinsufficiency 3, 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):

- **progressive familial intrahepatic cholestasis type 3** — Definitive (AR)

## Protein context {#protein}

Residue **769** lies in an α-helix; the abc transmembrane type-1 2 domain.

AlphaFold model confidence (whole protein): pLDDT 83.36, 48% of residues very-high.

**4 experimental structure(s)** (PDB): [6S7P](https://www.rcsb.org/structure/6S7P), [7NIU](https://www.rcsb.org/structure/7NIU), [7NIV](https://www.rcsb.org/structure/7NIV), [7NIW](https://www.rcsb.org/structure/7NIW).

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

*Describes the biological roles of ABCB4 (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:** ABCB4's established molecular role includes ATPase-coupled transmembrane transporter activity. p.Phe769fs falls in the abc transmembrane type-1 2 domain. In Reactome, ABCB4 is annotated in disease pathway(s) including **Defective ABCB4 causes PFIC3, ICP3 and GBD1**.

**Disease mechanism (Reactome):** ABCB4 loss or alteration is curated in [Defective ABCB4 causes PFIC3, ICP3 and GBD1](https://reactome.org/content/detail/R-HSA-5678771).

### Pathways affected {#pathways}

ABCB4 participates in **3 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective ABCB4 causes PFIC3, ICP3 and GBD1](https://reactome.org/content/detail/R-HSA-5678771) | curated |
| [ABC-family protein mediated transport](https://reactome.org/content/detail/R-HSA-382556) | curated |
| [PPARA activates gene expression](https://reactome.org/content/detail/R-HSA-1989781) | curated |

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

**Molecular function:** ATPase-coupled transmembrane transporter activity, phosphatidylcholine floppase activity.

**Biological process:** positive regulation of cholesterol transport, phospholipid translocation, lipid homeostasis, positive regulation of phospholipid translocation, cellular response to bile acid, positive regulation of phospholipid transport.

## Clinical significance {#significance}

**Pathogenic** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-01-01.

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

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Rolfs Rare Disease Consulting, Rolfs Consulting Und Verwaltungs GmbH | Pathogenic | criteria provided, single submitter | clinical testing | 2022-01-01 |

## Associated conditions {#conditions}

[progressive familial intrahepatic cholestasis type 3](https://sugi.bio/atlas/disease/progressive-familial-intrahepatic-cholestasis-type-3/).

**Reported phenotype names (ClinVar):** Progressive familial intrahepatic cholestasis type 3, Low Gamma-GT Familial Intrahepatic Cholestasis, MDR3 DEFICIENCY.

## Similar variants {#similar}

Related ABCB4 variant pages (same residue, condition, or type): [ABCB4 p.Asp682fs](/variant/abcb4-p-asp682fs), [ABCB4 p.Leu518fs](/variant/abcb4-p-leu518fs), [ABCB4 p.Lys1026fs](/variant/abcb4-p-lys1026fs), [ABCB4 p.Lys30fs](/variant/abcb4-p-lys30fs), [ABCB4 p.Phe769Tyr](/variant/abcb4-p-phe769tyr), [ABCB4 c.3081+2_3081+19del](/variant/abcb4-c-3081-plus-2-3081-plus-19del), [ABCB4 p.Ala262fs](/variant/abcb4-p-ala262fs), [ABCB4 p.Ala546fs](/variant/abcb4-p-ala546fs).

### 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 2687808). 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.*