# NM_000033.4(ABCD1):c.1679C>T (p.Pro560Leu)

https://sugi.bio/variant/abcd1-p-pro560leu

## Summary

**ABCD1 p.Pro560Leu (c.1679C>T)** is classified **Pathogenic** in ABCD1 (ClinVar, Multiple submitters, 13 submitters; last evaluated 2025-11-13). AlphaMissense: likely pathogenic (0.9559); Very rare (popmax 0.000112%, nfe); Associated with ABCD1-related disorder.

**At a glance:** Pathogenic · review: Multiple submitters · rsID rs398123105 · 13 submitters · 2 linked conditions · AlphaMissense likely pathogenic · very rare (popmax 0.000112%, nfe)

## For patients & families {#patients}

This is a change in the ABCD1 gene that is considered disease-causing, submitted by 13 submitters, and is linked to ABCD1-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 | [ABCD1](https://sugi.bio/atlas/gene/ABCD1/) |
| Protein change (HGVS p.) | p.Pro560Leu |
| Coding change (HGVS c.) | c.1679C>T |
| MANE Select transcript | [NM_000033](https://www.ncbi.nlm.nih.gov/nuccore/NM_000033) |
| dbSNP | [rs398123105](https://www.ncbi.nlm.nih.gov/snp/rs398123105/) |
| Variant type | single nucleotide variant |
| Location | chrX:153740618-153740618 (GRCh38) |
| ClinVar | [VCV92320](https://www.ncbi.nlm.nih.gov/clinvar/variation/92320/) |

**All HGVS expressions:** `LRG_1017:g.20751C>T`, `LRG_1017t1:c.1679C>T`, `NC_000023.10:g.153006072C>T`, `NC_000023.11:g.153740618C>T`, `NG_009022.2:g.20751C>T`, `NM_000033.4:c.1679C>T`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.9559) — concordant with the pathogenic call
- REVEL 0.897 (moderately pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -16.216 (damaging) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this damaging
- Conservation: phyloP 7.565, GERP 1.88, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 26.4**. 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 0.38** across the covering region of the MANE Select transcript (153,740,228–153,743,489), spanning 3,261 bp. Chi-square p 4e-11. 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 **0.000112%** (nfe) · 1/895,290 in the highest group · 1/1,096,432 alleles overall — very rare (popmax 0.000112%, nfe).

*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}

**ABCD1** population constraint: 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):

- **adrenoleukodystrophy** — Definitive (XL)

## Protein context {#protein}

Residue **560** lies in a UniProt-annotated variant site (in ald; cald-type); a UniProt-annotated variant site (in ald; amn and almd-types); a UniProt-annotated variant site (in ald); a turn; the abc transporter domain.

AlphaFold model confidence (whole protein): pLDDT 81.58, 43% of residues very-high.

**14 experimental structure(s)** (PDB): [7RR9](https://www.rcsb.org/structure/7RR9), [7RRA](https://www.rcsb.org/structure/7RRA), [7SHM](https://www.rcsb.org/structure/7SHM), [7SHN](https://www.rcsb.org/structure/7SHN), [7VR1](https://www.rcsb.org/structure/7VR1), [7VWC](https://www.rcsb.org/structure/7VWC).

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

*Describes the biological roles of ABCD1 (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:** ABCD1's established molecular role includes long-chain fatty acid transmembrane transporter activity. p.Pro560Leu falls in the abc transporter domain. In Reactome, ABCD1 is annotated in disease pathway(s) including **Defective ABCD1 causes ALD**.

**Disease mechanism (Reactome):** ABCD1 loss or alteration is curated in [Defective ABCD1 causes ALD](https://reactome.org/content/detail/R-HSA-5684045).

### Pathways affected {#pathways}

ABCD1 participates in **6 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective ABCD1 causes ALD](https://reactome.org/content/detail/R-HSA-5684045) | curated |
| [ABC transporters in lipid homeostasis](https://reactome.org/content/detail/R-HSA-1369062) | curated |
| [Beta-oxidation of very long chain fatty acids](https://reactome.org/content/detail/R-HSA-390247) | curated |
| [Class I peroxisomal membrane protein import](https://reactome.org/content/detail/R-HSA-9603798) | curated |
| [Linoleic acid (LA) metabolism](https://reactome.org/content/detail/R-HSA-2046105) | curated |
| [alpha-linolenic acid (ALA) metabolism](https://reactome.org/content/detail/R-HSA-2046106) | curated |

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

**Molecular function:** long-chain fatty acid transmembrane transporter activity, ATP binding, ABC-type fatty-acyl-CoA transporter activity, ATP hydrolysis activity, enzyme binding, ATPase-coupled transmembrane transporter activity.

**Biological process:** very long-chain fatty acid metabolic process, fatty acid beta-oxidation, peroxisome organization, long-chain fatty acid import into peroxisome, positive regulation of fatty acid beta-oxidation, very long-chain fatty-acyl-CoA catabolic process.

## Clinical significance {#significance}

**Pathogenic** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-11-13.

**Submitter consensus:** unanimous (13/13 Pathogenic).

**Submission history:** 13 submissions (2013–2025); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre | Pathogenic | criteria provided, single submitter | clinical testing | 2023-05-12 |
| Eurofins Ntd Llc (ga) | Pathogenic | criteria provided, single submitter | clinical testing | 2013-04-30 |
| GeneDx | Pathogenic | criteria provided, single submitter | clinical testing | 2025-11-13 |
| Genome-Nilou Lab | Pathogenic | criteria provided, single submitter | clinical testing | 2021-11-07 |
| Baylor Genetics | Pathogenic | criteria provided, single submitter | clinical testing | 2022-12-04 |
| Intergen Genetics and Rare Diseases Diagnosis Center | Pathogenic | criteria provided, single submitter | clinical testing | 2023-08-15 |
| Ambry Genetics | Pathogenic | criteria provided, single submitter | clinical testing | 2017-10-10 |
| Blueprint Genetics | Pathogenic | criteria provided, single submitter | clinical testing | 2021-09-08 |
| Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Pathogenic | criteria provided, single submitter | clinical testing | 2022-05-13 |
| Clinical Genetics Laboratory, Skane University Hospital Lund | Pathogenic | criteria provided, single submitter | clinical testing | 2022-07-13 |
| Revvity Omics, Revvity | Pathogenic | criteria provided, single submitter | clinical testing | 2024-12-09 |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2024-12-19 |
| Natera, Inc. | Pathogenic | criteria provided, single submitter | clinical testing | 2025-09-12 |

## Associated conditions {#conditions}

[ABCD1-related disorder](https://sugi.bio/atlas/disease/abcd1-related-disorder/), [adrenoleukodystrophy](https://sugi.bio/atlas/disease/adrenoleukodystrophy/).

**Reported phenotype names (ClinVar):** ABCD1-related disorder, Adrenoleukodystrophy, not provided, Inborn genetic diseases, ABCD1-related condition, none provided, X-Linked Adrenoleukodystrophy, ADDISON DISEASE AND CEREBRAL SCLEROSIS, BRONZE SCHILDER DISEASE, MELANODERMIC LEUKODYSTROPHY.

## Same-residue context {#hotspot}

Residue **560** carries **3 other pathogenic ClinVar variants** — a recurrently-mutated position: [ABCD1 p.Pro560Arg](/variant/abcd1-p-pro560arg), [ABCD1 p.Pro560Ser](/variant/abcd1-p-pro560ser), [ABCD1 p.Pro560Thr](/variant/abcd1-p-pro560thr). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related ABCD1 variant pages (same residue, condition, or type): [ABCD1 p.Pro560=](/variant/abcd1-p-pro560), [ABCD1 p.Pro560Arg](/variant/abcd1-p-pro560arg), [ABCD1 p.Pro560Ser](/variant/abcd1-p-pro560ser), [ABCD1 p.Pro560Thr](/variant/abcd1-p-pro560thr), [ABCD1 c.1635-2A>G](/variant/abcd1-c-1635-minus-2a-g), [ABCD1 c.1781-1G>C](/variant/abcd1-c-1781-minus-1g-c), [ABCD1 c.1781-1G>T](/variant/abcd1-c-1781-minus-1g-t), [ABCD1 c.1866-10G>A](/variant/abcd1-c-1866-minus-10g-a).

### 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 92320). 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.*