Is F10 p.Thr264= (c.792C>T) pathogenic?

F10 p.Thr264= (c.792C>T) is classified Benign in F10 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2024-11-27). Common (popmax 86.8%, nfe) — too common for a highly-penetrant pathogenic allele; Associated with congenital factor X deficiency.

What condition is associated with F10 p.Thr264= (c.792C>T)?

F10 p.Thr264= (c.792C>T) is associated with congenital factor X deficiency (ClinVar).

How is Congenital factor X deficiency inherited?

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

F10 p.Thr264=

Q: How common is F10 p.Thr264= (c.792C>T) in the general population?

F10 p.Thr264= (c.792C>T) is common (popmax 86.8%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.792C>T · rs5960 · VCV256308

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Common

common (popmax 86.8%, nfe) — too common for a highly-penetrant pathogenic allele

Conditions

congenital factor X deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.3	GERP -0.59, phastCons 1
Overall
CADD	7.255	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 86.8% European (non-Finnish) · 1,023,301/1,178,984 alleles

Filtering AF 86.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 86.6%

Overall 82.1% 1,323,433/1,612,706 alleles · common exomes 1,213,187/1,460,660 · genomes 110,246/152,046 · joint denominator

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	94.2%	1
Ashkenazi Jewishnot grpmax-eligible	88.4%	1
European (non-Finnish)grpmax	86.8%	1
Middle Eastern	85.4%	1
Finnishnot grpmax-eligible	82.4%	1
Remaining individualsnot grpmax-eligible	79.9%	1
South Asian	71.2%	1
Admixed American	65.8%	2
East Asian	54.2%	2
African / African-American	49%	2

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: F10
Protein: p.Thr264=
Coding: c.792C>T
MANE Select: NM_000504
dbSNP: rs5960
Type: single nucleotide variant
Location: chr13:113147423 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.47 · 192 PDB
Residue 264: the peptidase s1 domain; a β-strand

Full F10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

congenital factor X deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Congenital factor X deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

F10 p.Glu54Gly Likely pathogenic ★★ same condition
F10 p.Gly363Ser Likely pathogenic ★★ same condition
F10 p.Gly450Arg Likely pathogenic ★★ same condition
F10 p.Arg291Gln Uncertain significance ★★ ⚠ same condition
F10 p.Glu306Lys Uncertain significance ★★ ⚠ same condition
F10 p.Gly106= Uncertain significance ★★ same condition
F10 p.Gly154Arg Uncertain significance ★★ ⚠ same condition
F10 p.Pro472Leu Uncertain significance ★★ ⚠ 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/f10-p-thr264 (accessed [today's date]).

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