# NM_000130.5(F5):c.1601= (p.Arg534=)

https://sugi.bio/variant/f5-p-arg534

## Summary

**F5 p.Arg534= (c.1601=)** is classified **Conflicting classifications of pathogenicity** in F5 (ClinVar, Conflicting submitters, 6 submitters; last evaluated 2026-02-04). Absent from gnomAD v4.1; Associated with F5-related disorders.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs6025 · 6 submitters · 2 linked conditions · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the F5 gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 6 submitters, and is linked to F5-related disorders.

*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 | [F5](https://sugi.bio/atlas/gene/F5/) |
| Protein change (HGVS p.) | p.Arg534= |
| Coding change (HGVS c.) | c.1601= |
| MANE Select transcript | [NM_000130](https://www.ncbi.nlm.nih.gov/nuccore/NM_000130) |
| dbSNP | [rs6025](https://www.ncbi.nlm.nih.gov/snp/rs6025/) |
| Variant type | single nucleotide variant |
| Location | chr1:169549811-169549811 (GRCh38) |
| ClinVar | [VCV226007](https://www.ncbi.nlm.nih.gov/clinvar/variation/226007/) |

**All HGVS expressions:** `LRG_553:g.41721=`, `LRG_553t1:c.1601=`, `LRG_553t1:c.1601G>G`, `NC_000001.10:g.169519049T>C`, `NC_000001.11:g.169549811=`, `NG_011806.1:g.41721=`, `NM_000130.5:c.1601=`

## 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 7.658, GERP 1.61, phastCons 1 — highly conserved position (PP3-type support)
- SpliceAI: **below the reporting threshold**. This position is scored for a different substitution (C>A, Δ0.31 donor 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: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*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}

**F5** population constraint: LOEUF 0.704, pLI 5.2212e-24, missense-Z 2.7865. *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):

- **thrombophilia due to activated protein C resistance** — Definitive (AD)
- **congenital factor V deficiency** — Definitive (AR)

## Protein context {#protein}

Residue **534** lies in a UniProt-annotated variant site (in thph2; factor v leiden; risk factor for budd-chiari syndrome; risk factor for ischemic stroke); a β-strand; a functional site (cleavage; by activated protein c); the f5/8 type a 2 domain.

AlphaFold model confidence (whole protein): pLDDT 62.57, 22% of residues very-high.

**23 experimental structure(s)** (PDB): [1CZS](https://www.rcsb.org/structure/1CZS), [1CZT](https://www.rcsb.org/structure/1CZT), [1CZV](https://www.rcsb.org/structure/1CZV), [36JA](https://www.rcsb.org/structure/36JA), [36JB](https://www.rcsb.org/structure/36JB), [3P6Z](https://www.rcsb.org/structure/3P6Z).

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

*Describes the biological roles of F5 (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:** p.Arg534= falls in the f5/8 type a 2 domain. In Reactome, F5 is annotated in disease pathway(s) including **Defective cleavage of FV variant at R334**, **Defective cleavage of FV variant at a.a.534 **.

**Disease mechanism (Reactome):** F5 loss or alteration is curated in [Defective cleavage of FV variant at R334](https://reactome.org/content/detail/R-HSA-9930479), [Defective cleavage of FV variant at a.a.534 ](https://reactome.org/content/detail/R-HSA-9930449).

### Pathways affected {#pathways}

F5 participates in **11 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Defective cleavage of FV variant at R334](https://reactome.org/content/detail/R-HSA-9930479) | curated |
| ⚕ [Defective cleavage of FV variant at a.a.534 ](https://reactome.org/content/detail/R-HSA-9930449) | curated |
| [Amplification and propagation of coagulation cascade](https://reactome.org/content/detail/R-HSA-9769743) | curated |
| [COPII-mediated vesicle transport](https://reactome.org/content/detail/R-HSA-204005) | curated |
| [Cargo concentration in the ER](https://reactome.org/content/detail/R-HSA-5694530) | curated |
| [Initiation of coagulation cascade](https://reactome.org/content/detail/R-HSA-9769735) | curated |
| [Platelet degranulation ](https://reactome.org/content/detail/R-HSA-114608) | curated |
| [Post-translational protein phosphorylation](https://reactome.org/content/detail/R-HSA-8957275) | curated |
| [Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)](https://reactome.org/content/detail/R-HSA-381426) | curated |
| [Regulation of clotting cascade](https://reactome.org/content/detail/R-HSA-9769739) | curated |
| [None](https://reactome.org/content/detail/R-HSA-140875) | other |

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2026-02-04.

**Submitter consensus:** conflicting (3 Benign, 3 Pathogenic).

**Submission history:** 6 submissions (2018–2026); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| GeneDx | Benign | criteria provided, single submitter | clinical testing | 2018-06-16 |
| Breakthrough Genomics, Breakthrough Genomics | Benign | criteria provided, single submitter | not provided |  |
| Blueprint Genetics | Pathogenic | criteria provided, single submitter | clinical testing | 2024-11-26 |
| Department of Pathology and Laboratory Medicine, Sinai Health System | Pathogenic | no assertion criteria provided | clinical testing |  |
| CeGaT Center for Human Genetics Tuebingen | Pathogenic | criteria provided, single submitter | clinical testing | 2022-02-01 |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2026-02-04 |

## Associated conditions {#conditions}

[F5-related disorders](https://sugi.bio/atlas/disease/f5-related-disorders/), [congenital factor V deficiency](https://sugi.bio/atlas/disease/congenital-factor-v-deficiency/).

**Reported phenotype names (ClinVar):** F5-related disorders, not provided, Congenital factor V deficiency, none provided, Hereditary factor V deficiency disease, LABILE FACTOR DEFICIENCY, OWREN PARAHEMOPHILIA, PARAHEMOPHILIA.

## Same-residue context {#hotspot}

Residue **534** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [F5 p.Arg534Ter](/variant/f5-p-arg534ter). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Pharmacogenomics (PharmGKB) {#pgx}

Clinical drug-response annotations:

| Drug(s) | Evidence level | Category | Phenotype |
| --- | --- | --- | --- |
| hormonal contraceptives for systemic use | 2B | Toxicity | Thrombotic disease |
*PharmGKB levels 1A/1B (highest) → 4. Discuss any medication decision with your prescriber — reference information, not advice.*

## Similar variants {#similar}

Related F5 variant pages (same residue, condition, or type): [F5 p.Arg534Ter](/variant/f5-p-arg534ter), [F5 c.1297-2A>G](/variant/f5-c-1297-minus-2a-g), [F5 p.Arg1030Ter](/variant/f5-p-arg1030ter), [F5 p.Arg146Ter](/variant/f5-p-arg146ter), [F5 p.Arg1621Ter](/variant/f5-p-arg1621ter), [F5 p.Arg1634Ter](/variant/f5-p-arg1634ter), [F5 p.Arg2102His](/variant/f5-p-arg2102his), [F5 p.Arg740Ter](/variant/f5-p-arg740ter).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); 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 2026-10-14); 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 226007). 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.*