# NM_000090.4(COL3A1):c.1460C>T (p.Ala487Val)

https://sugi.bio/variant/col3a1-p-ala487val

## Summary

**COL3A1 p.Ala487Val (c.1460C>T)** is classified **Conflicting classifications of pathogenicity** in COL3A1 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-02-03). AlphaMissense: likely benign (0.0695); Ultra-rare (popmax 0.011%, sas); Associated with familial thoracic aortic aneurysm and aortic dissection.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs770157568 · 4 submitters · 2 linked conditions · AlphaMissense likely benign · ultra-rare (popmax 0.011%, sas)

## For patients & families {#patients}

This is a change in the COL3A1 gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 4 submitters, and is linked to familial thoracic aortic aneurysm and aortic dissection.

*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) | Adolescent, Adult, Childhood |
| Clinical trials | 2 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | COL3A1 is a diagnostic-grade gene on 11 Genomics England panels |

**Commonly reported features of Familial thoracic aortic aneurysm and aortic dissection** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Cutis marmorata — Very frequent (99-80%)
- Abnormality of connective tissue — Very frequent (99-80%)
- Cystic medial necrosis of the aorta — Very frequent (99-80%)
- Abnormality iris morphology — Frequent (79-30%)
- Hypertension — Frequent (79-30%)
- Cardiomegaly — Frequent (79-30%)
- Aortic regurgitation — Frequent (79-30%)
- Coronaryartery atherosclerosis — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0002249/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [COL3A1](https://sugi.bio/atlas/gene/COL3A1/) |
| Protein change (HGVS p.) | p.Ala487Val |
| Coding change (HGVS c.) | c.1460C>T |
| MANE Select transcript | [NM_000090](https://www.ncbi.nlm.nih.gov/nuccore/NM_000090) |
| dbSNP | [rs770157568](https://www.ncbi.nlm.nih.gov/snp/rs770157568/) |
| Variant type | single nucleotide variant |
| Location | chr2:188995050-188995050 (GRCh38) |
| ClinVar | [VCV2775106](https://www.ncbi.nlm.nih.gov/clinvar/variation/2775106/) |

**All HGVS expressions:** `LRG_3:g.25678C>T`, `LRG_3t1:c.1460C>T`, `NC_000002.11:g.189859776C>T`, `NC_000002.12:g.188995050C>T`, `NG_007404.1:g.25678C>T`, `NM_000090.4:c.1460C>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- AlphaMissense **likely benign** (0.0695)
- REVEL 0.153 (moderately benign-leaning) — agrees with AlphaMissense
- SaProt LLR -8.592 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP -1.68, GERP 0.039 — not a conserved position (phyloP < 0.1, ACGS BP7 cut)
- CADD: **PHRED 14.98**. 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 0.68** across the covering region of the MANE Select transcript (188,984,854–188,996,451), spanning 11,597 bp. Chi-square p 4.3e-17. 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 **0.011%** (sas) · FAF95 0.00594% · FAF99 0.00453% · 10/91,070 in the highest group · 10/1,614,054 alleles overall — ultra-rare (popmax 0.011%, sas).

*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}

**COL3A1** population constraint: LOEUF 0.291, pLI 1, missense-Z 4.6137; 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):

- **Ehlers-Danlos syndrome, vascular type** — Definitive (AD)

## Protein context {#protein}

Residue **487** lies in a UniProt-annotated variant site (in pmgedsv); the 'disordered' region; the 'triple-helical region' region.

AlphaFold model confidence (whole protein): pLDDT 54.98, 19% of residues very-high.

**11 experimental structure(s)** (PDB): [2V53](https://www.rcsb.org/structure/2V53), [3DMW](https://www.rcsb.org/structure/3DMW), [4AE2](https://www.rcsb.org/structure/4AE2), [4AEJ](https://www.rcsb.org/structure/4AEJ), [4AK3](https://www.rcsb.org/structure/4AK3), [4GYX](https://www.rcsb.org/structure/4GYX).

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

*Describes the biological roles of COL3A1 (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:** COL3A1's established molecular role includes protease binding. p.Ala487Val falls in the disordered region.


### Pathways affected {#pathways}

COL3A1 participates in **16 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Assembly of collagen fibrils and other multimeric structures](https://reactome.org/content/detail/R-HSA-2022090) | curated |
| [Collagen biosynthesis and modifying enzymes](https://reactome.org/content/detail/R-HSA-1650814) | curated |
| [Collagen chain trimerization](https://reactome.org/content/detail/R-HSA-8948216) | curated |
| [Developmental Lineage of Pancreatic Ductal Cells](https://reactome.org/content/detail/R-HSA-9925563) | curated |
| [Developmental Lineage of Pancreatic Endocrine Mid Progenitor Cells](https://reactome.org/content/detail/R-HSA-9981148) | curated |
| [Fibronectin matrix formation](https://reactome.org/content/detail/R-HSA-1566977) | curated |
| [Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell](https://reactome.org/content/detail/R-HSA-198933) | curated |
| [Integrin cell surface interactions](https://reactome.org/content/detail/R-HSA-216083) | curated |
| [MET activates PTK2 signaling](https://reactome.org/content/detail/R-HSA-8874081) | curated |
| [NCAM1 interactions](https://reactome.org/content/detail/R-HSA-419037) | curated |
| [Non-integrin membrane-ECM interactions](https://reactome.org/content/detail/R-HSA-3000171) | curated |
| [Signaling by PDGF](https://reactome.org/content/detail/R-HSA-186797) | curated |
| [Collagen degradation](https://reactome.org/content/detail/R-HSA-1442490) | electronic |
| [ECM proteoglycans](https://reactome.org/content/detail/R-HSA-3000178) | electronic |
| [Scavenging by Class A Receptors](https://reactome.org/content/detail/R-HSA-3000480) | electronic |
| [Syndecan interactions](https://reactome.org/content/detail/R-HSA-3000170) | electronic |

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

**Molecular function:** protease binding, integrin binding, extracellular matrix structural constituent, extracellular matrix structural constituent conferring tensile strength, platelet-derived growth factor binding.

**Biological process:** cell-matrix adhesion, transforming growth factor beta receptor signaling pathway, integrin-mediated signaling pathway, heart development, response to radiation, peptide cross-linking.

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2026-02-03.

**Submitter consensus:** conflicting (2 Uncertain significance, 1 Likely benign, 1 Uncertain Significance).

**Submission history:** 4 submissions (2024–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Ambry Genetics | Likely benign | criteria provided, single submitter | clinical testing | 2024-05-31 |
| All of Us Research Program, National Institutes of Health | Uncertain Significance | criteria provided, single submitter | clinical testing | 2024-03-05 |
| Color Diagnostics, LLC DBA Color Health | Uncertain significance | criteria provided, single submitter | clinical testing | 2024-03-07 |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2026-02-03 |

## Associated conditions {#conditions}

[familial thoracic aortic aneurysm and aortic dissection](https://sugi.bio/atlas/disease/familial-thoracic-aortic-aneurysm-and-aortic-dissection/), [Ehlers-Danlos syndrome, vascular type](https://sugi.bio/atlas/disease/ehlers-danlos-syndrome-vascular-type/).

**Reported phenotype names (ClinVar):** Familial thoracic aortic aneurysm and aortic dissection, Ehlers-Danlos syndrome, type 4, Thoracic aortic aneurysms and dissections, Ehlers-Danlos syndrome vascular type, Ehlers Danlos syndrome, ecchymotic type, Ehlers Danlos syndrome, arterial type, Ehlers Danlos syndrome, Sack-Barabas type, Ehlers-Danlos Syndrome Type IV.

## Similar variants {#similar}

Related COL3A1 variant pages (same residue, condition, or type): [COL3A1 p.Ala487Ser](/variant/col3a1-p-ala487ser), [COL3A1 p.Ala487=](/variant/col3a1-p-ala487), [COL3A1 c.1051-1G>C](/variant/col3a1-c-1051-minus-1g-c), [COL3A1 c.1294-1G>A](/variant/col3a1-c-1294-minus-1g-a), [COL3A1 c.1347+1G>A](/variant/col3a1-c-1347-plus-1g-a), [COL3A1 c.1348-2A>G](/variant/col3a1-c-1348-minus-2a-g), [COL3A1 c.1662+1G>A](/variant/col3a1-c-1662-plus-1g-a), [COL3A1 c.1663-1G>A](/variant/col3a1-c-1663-minus-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 2775106). 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.*