Is F8 p.Phe312Ser (c.935T>C) pathogenic?

F8 p.Phe312Ser (c.935T>C) is classified Pathogenic/Likely pathogenic in F8 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-03-12). AlphaMissense: likely pathogenic (0.7711); Very rare (popmax 0.000112%, nfe); Associated with hemophilia B.

What condition is associated with F8 p.Phe312Ser (c.935T>C)?

F8 p.Phe312Ser (c.935T>C) is associated with hemophilia B, hemophilia A (ClinVar).

How common is F8 p.Phe312Ser (c.935T>C) in the general population?

F8 p.Phe312Ser (c.935T>C) is very rare (popmax 0.000112%, nfe) (gnomAD).

How is Hemophilia B inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about F8 p.Phe312Ser (c.935T>C)?

AlphaMissense predicts likely pathogenic (score 0.7711) — an in-silico prediction, not a clinical call.

F8 p.Phe312Ser

c.935T>C · rs137852405 · VCV10196

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

likely pathogenic

0.7711 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000112%, nfe)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hemophilia B

Computational evidence

Protein change
AlphaMissense	0.7711	likely pathogenic ✓ concordant with ClinVar · top 10% in F8
REVEL	0.857	moderately pathogenic-leaning
SaProt	LLR -5.71	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.6, phastCons 1
Regional constraint	o/e 0.74	unconstrained · MANE · 38 kb · p 2.6e-06 · regional, not allelic
Overall
CADD	25.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000112% European (non-Finnish) · 1/895,416 alleles

Overall 9.11e-05% 1/1,098,091 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: F8
Protein: p.Phe312Ser
Coding: c.935T>C
MANE Select: NM_000132
dbSNP: rs137852405
Type: single nucleotide variant
Location: chrX:154969405 (GRCh38)
Structure: AlphaFold pLDDT 61.20 · 29 PDB
Residue 312: a UniProt-annotated variant site (in hema; mild/moderate); a disulfide bond; a β-strand; the f5/8 type a 1 domain; the plastocyanin-like 2 domain

Full F8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hemophilia B — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: hemophilia A

For Hemophilia B (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

F8 c.6429+2T>A Pathogenic ★★★ same condition
F8 p.Ala111Thr Likely pathogenic ★★★ same condition
F8 p.Ala2220Pro Pathogenic ★★★ same condition
F8 p.Ala415Asp Likely pathogenic ★★★ same condition
F8 p.Ala415Val Pathogenic ★★★ ⚠ same condition
F8 p.Arg1768His Pathogenic ★★★ ⚠ same condition
F8 p.Arg1800His Pathogenic ★★★ same condition
F8 p.Arg2016Trp Pathogenic ★★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/f8-p-phe312ser (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown