# NM_000501.4(ELN):c.1317C>T (p.Pro439=)

https://sugi.bio/variant/eln-p-pro439

## Summary

**ELN p.Pro439= (c.1317C>T)** is classified **Benign/Likely benign** in ELN (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-09-23). Ultra-rare (popmax 0.0825%, mid); Associated with cutis laxa, autosomal dominant 1.

**At a glance:** Benign/Likely benign · review: Multiple submitters · rsID rs201861098 · 4 submitters · 2 linked conditions · ultra-rare (popmax 0.0825%, mid)

## For patients & families {#patients}

This is a change in the ELN gene that is classified as benign/likely benign — not considered disease-causing, submitted by 4 submitters, and is linked to cutis laxa, autosomal dominant 1.

*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 dominant |
| Age of onset (of this condition) | Infancy, Neonatal |
| Diagnostic panels | ELN is a diagnostic-grade gene on 8 Genomics England panels |

**Commonly reported features of Autosomal dominant cutis laxa** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Cutis laxa — Very frequent (99-80%)
- Hyperextensible skin — Very frequent (99-80%)
- Redundant skin — Very frequent (99-80%)
- Increased number of skin folds — Very frequent (99-80%)
- Fragmented elastic fibers in the dermis — Very frequent (99-80%)
- Premature skin wrinkling — Very frequent (99-80%)
- Joint hypermobility — Frequent (79-30%)
- Inguinal hernia — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0015055/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [ELN](https://sugi.bio/atlas/gene/ELN/) |
| Protein change (HGVS p.) | p.Pro439= |
| Coding change (HGVS c.) | c.1317C>T |
| MANE Select transcript | [NM_000501](https://www.ncbi.nlm.nih.gov/nuccore/NM_000501) |
| dbSNP | [rs201861098](https://www.ncbi.nlm.nih.gov/snp/rs201861098/) |
| Variant type | single nucleotide variant |
| Location | chr7:74056673-74056673 (GRCh38) |
| ClinVar | [VCV360652](https://www.ncbi.nlm.nih.gov/clinvar/variation/360652/) |

**All HGVS expressions:** `NC_000007.13:g.73471003C>T`, `NC_000007.14:g.74056673C>T`, `NG_009261.1:g.33577C>T`, `NM_000501.4:c.1317C>T`, `NM_001081752.3:c.1287C>T`, `NM_001081753.3:c.1332C>T`, `NM_001081754.3:c.1332C>T`, `NM_001081755.3:c.1317C>T`, `NM_001278912.2:c.1317C>T`, `NM_001278913.2:c.1131C>T`, `NM_001278914.2:c.1302C>T`, `NM_001278915.2:c.1317C>T`, `NM_001278916.2:c.1275C>T`, `NM_001278917.2:c.1287C>T`, `NM_001278918.2:c.1107C>T`, `NM_001278939.2:c.1317C>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 -0.187, GERP -2.22, phastCons 0.134 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 5.686**. 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: **below the reporting threshold**. This position is scored for a different substitution (C>A, Δ0.90 acceptor gain), so this allele was evaluated and its deltas all fell under Δ0.2 — a prediction of no splicing effect for this allele, not a gap in our data. *No ACMG code assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.0825%** (mid) · FAF95 0.0324% · FAF99 0.026% · 5/6,062 in the highest group · 107/1,613,792 alleles overall — ultra-rare (popmax 0.0825%, mid).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Middle Eastern (grpmax) | 0.0825% | 1,212 |
| African / African-American | 0.0413% | 2,420 |
| South Asian | 0.00659% | 15,179 |
| Remaining individuals (not grpmax-eligible) | 0.0064% | 15,625 |
| European (non-Finnish) | 0.005% | 20,001 |
| East Asian | 0.00223% | 44,864 |
| Finnish (not grpmax-eligible) | 0.00157% | 63,710 |

*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}

**ELN** population constraint: LOEUF 0.696, pLI 7.6169e-10, missense-Z 1.2583; ClinGen dosage — haploinsufficiency 3/3, triplosensitivity 0/3. *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):

- **cutis laxa, autosomal dominant 1** — Definitive (AD)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 36.20, 0% of residues very-high.

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

*Describes the biological roles of ELN (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.*


### Pathways affected {#pathways}

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

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Degradation of the extracellular matrix](https://reactome.org/content/detail/R-HSA-1474228) | curated |
| [Elastic fibre formation](https://reactome.org/content/detail/R-HSA-1566948) | curated |
| [Molecules associated with elastic fibres](https://reactome.org/content/detail/R-HSA-2129379) | electronic |

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

**Biological process:** outflow tract morphogenesis.

## Clinical significance {#significance}

**Benign/Likely benign** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-09-23.

**Submitter consensus:** conflicting (4 Likely benign, 1 Benign).

**Submission history:** 5 submissions (2018–2025); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Benign | criteria provided, single submitter | clinical testing | 2018-01-13 |
| Illumina Laboratory Services, Illumina | Likely benign | criteria provided, single submitter | clinical testing | 2018-01-13 |
| Breakthrough Genomics, Breakthrough Genomics | Likely benign | criteria provided, single submitter | not provided |  |
| Blueprint Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-10-09 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2025-09-23 |

## Associated conditions {#conditions}

[cutis laxa, autosomal dominant 1](https://sugi.bio/atlas/disease/cutis-laxa-autosomal-dominant-1/), [supravalvular aortic stenosis](https://sugi.bio/atlas/disease/supravalvular-aortic-stenosis/).

**Reported phenotype names (ClinVar):** Cutis laxa, autosomal dominant 1, Supravalvar aortic stenosis, not provided, not specified, AllHighlyPenetrant, none provided, ELN-Related Cutis Laxa, Supravalvar aortic stenosis, Eisenberg type.

## Similar variants {#similar}

Related ELN variant pages (same residue, condition, or type): [ELN p.Pro439Ser](/variant/eln-p-pro439ser), [ELN c.377-2A>G](/variant/eln-c-377-minus-2a-g), [ELN c.643+1G>C](/variant/eln-c-643-plus-1g-c), [ELN c.686-2A>G](/variant/eln-c-686-minus-2a-g), [ELN c.800-1G>A](/variant/eln-c-800-minus-1g-a), [ELN c.800-2A>G](/variant/eln-c-800-minus-2a-g), [ELN c.800-3C>G](/variant/eln-c-800-minus-3c-g), [ELN c.82+1G>A](/variant/eln-c-82-plus-1g-a).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); 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 2026-10-14); 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 360652). 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.*