Is F8 p.Thr154Pro (c.460A>C) pathogenic?

F8 p.Thr154Pro (c.460A>C) is classified Likely pathogenic in F8 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-02-01). AlphaMissense: ambiguous (0.3897); Absent from gnomAD v4.1; Associated with hemophilia B.

What condition is associated with F8 p.Thr154Pro (c.460A>C)?

F8 p.Thr154Pro (c.460A>C) is associated with hemophilia B (ClinVar).

How common is F8 p.Thr154Pro (c.460A>C) in the general population?

F8 p.Thr154Pro (c.460A>C) is absent from gnomAD v4.1 (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.Thr154Pro (c.460A>C)?

AlphaMissense predicts ambiguous (score 0.3897) — an in-silico prediction, not a clinical call.

F8 p.Thr154Pro

c.460A>C · rs1603436436 · VCV627312

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3897 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

hemophilia B

Computational evidence

Protein change
AlphaMissense	0.3897	ambiguous
REVEL	0.923	moderately pathogenic-leaning
SaProt	LLR -15.45	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 1.7, phastCons 1
Regional constraint	o/e 0.56	unconstrained · MANE · 53 kb · p 1.5e-11 · 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: F8
Protein: p.Thr154Pro
Coding: c.460A>C
MANE Select: NM_000132
dbSNP: rs1603436436
Type: single nucleotide variant
Location: chrX:154993077 (GRCh38)
Structure: AlphaFold pLDDT 61.20 · 29 PDB
Residue 154: a β-strand; the f5/8 type a 1 domain; the plastocyanin-like 1 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

For Hemophilia B (Orphanet):

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

Similar variants

F8 p.Thr154Lys Uncertain significance ★★ ⚠ same residue
F8 p.Thr154Ile Uncertain significance ★ ⚠ same residue
F8 p.Thr154Ala Likely pathogenic ⚠ same residue
F8 p.Arg602Ter Pathogenic ★★★ same condition
F8 p.Arg612Cys Pathogenic ★★★ ⚠ same condition
F8 p.Asn1739= Likely pathogenic ★★★ same condition
F8 p.Leu327Val Pathogenic ★★★ ⚠ same condition
F8 p.Trp2248Cys 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-thr154pro (accessed [today's date]).

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