# NM_000130.5(F5):c.2862del (p.Ser955fs)

https://sugi.bio/variant/f5-p-ser955fs

## Summary

**F5 p.Ser955fs (c.2862del)** is classified **Pathogenic/Likely pathogenic** in F5 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2023-05-15). Ultra-rare (popmax 0.0285%, sas); Associated with factor V deficiency.

**At a glance:** Pathogenic/Likely pathogenic · review: Multiple submitters · rsID rs765982916 · 4 submitters · 2 linked conditions · ultra-rare (popmax 0.0285%, sas)

## For patients & families {#patients}

This is a change in the F5 gene that is considered likely disease-causing, submitted by 4 submitters, and is linked to factor V deficiency.

*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:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0025179/index) · [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.Ser955fs |
| Coding change (HGVS c.) | c.2862del |
| MANE Select transcript | [NM_000130](https://www.ncbi.nlm.nih.gov/nuccore/NM_000130) |
| dbSNP | [rs765982916](https://www.ncbi.nlm.nih.gov/snp/rs765982916/) |
| Variant type | Deletion |
| Location | chr1:169542228-169542228 (GRCh38) |
| ClinVar | [VCV627051](https://www.ncbi.nlm.nih.gov/clinvar/variation/627051/) |

**All HGVS expressions:** `LRG_553:g.49304del`, `NC_000001.10:g.169511466del`, `NC_000001.11:g.169542228del`, `NG_011806.1:g.49304del`, `NM_000130.4:c.2862delT`, `NM_000130.5:c.2862del`

## 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 1.501, GERP 1.89, phastCons 0.012 — weakly conserved position
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. Gene population constraint: LOEUF 0.704, pLI 5.2212e-24. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 13 of 25**, so the transcript is predicted to undergo NMD.
- CADD: **PHRED 20.8**. 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: **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 (gnomAD v4.1): grpmax **0.0285%** (sas) · FAF95 0.0199% · FAF99 0.0171% · 26/91,082 in the highest group · 39/1,614,108 alleles overall — ultra-rare (popmax 0.0285%, sas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| South Asian (grpmax) | 0.0285% | 3,503 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,508 |
| Finnish (not grpmax-eligible) | 0.00156% | 64,038 |
| European (non-Finnish) | 0.000932% | 107,272 |

*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 **955** lies in the 'b' region.

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.Ser955fs falls in the b region. 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}

**Pathogenic/Likely pathogenic** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2023-05-15.

**Submitter consensus:** conflicting (3 Pathogenic, 1 Likely pathogenic).

**Submission history:** 4 submissions (2002–2023); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| OMIM | Pathogenic | no assertion criteria provided | literature only | 2002-01-15 |
| NIHR Bioresource Rare Diseases, University of Cambridge | Likely pathogenic | criteria provided, single submitter | research | 2019-02-01 |
| Department of Pathology and Laboratory Medicine, Sinai Health System | Pathogenic | criteria provided, single submitter | research | 2023-05-15 |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2023-04-12 |

## Associated conditions {#conditions}

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

**Reported phenotype names (ClinVar):** Factor V deficiency, Congenital factor V deficiency, Reduced coagulation factor V activity, PARAHEMOPHILIA, Hereditary factor V deficiency disease, LABILE FACTOR DEFICIENCY, OWREN PARAHEMOPHILIA.

## Similar variants {#similar}

Related F5 variant pages (same residue, condition, or type): [F5 p.Ser955Ile](/variant/f5-p-ser955ile), [F5 c.4962_4971+3del](/variant/f5-c-4962-4971-plus-3del), [F5 p.Ile847fs](/variant/f5-p-ile847fs), [F5 p.Leu1267fs](/variant/f5-p-leu1267fs), [F5 p.Leu1818fs](/variant/f5-p-leu1818fs), [F5 p.Lys674fs](/variant/f5-p-lys674fs), [F5 p.Thr397_Tyr399del](/variant/f5-p-thr397-tyr399del), [F5 c.251-6del](/variant/f5-c-251-minus-6del).

### 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 627051). 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.*