Is F10 p.Asp132= (c.396C>T) pathogenic?

F10 p.Asp132= (c.396C>T) is classified Benign/Likely benign in F10 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2024-09-17). Rare (popmax 0.894%, afr); Associated with congenital factor X deficiency.

What condition is associated with F10 p.Asp132= (c.396C>T)?

F10 p.Asp132= (c.396C>T) is associated with congenital factor X deficiency (ClinVar).

How common is F10 p.Asp132= (c.396C>T) in the general population?

F10 p.Asp132= (c.396C>T) is rare (popmax 0.894%, afr) (gnomAD).

How is Congenital factor X deficiency inherited?

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

F10 p.Asp132=

c.396C>T · rs111737184 · VCV311273

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.894%, afr)

Conditions

congenital factor X deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.92	GERP 1.3, phastCons 1
Overall
CADD	9.211	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.894% African / African-American · 671/75,074 alleles

Filtering AF 0.838% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.815%

Overall 0.0467% 754/1,614,142 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.894%	112
Middle Eastern	0.066%	1,516
Remaining individualsnot grpmax-eligible	0.0656%	1,525
Admixed American	0.0383%	2,610
South Asian	0.00329%	30,363
European (non-Finnish)	0.00102%	98,338

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.Asp132=
Coding: c.396C>T
MANE Select: NM_000504
dbSNP: rs111737184
Type: single nucleotide variant
Location: chr13:113140944 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.47 · 192 PDB
Residue 132: an α-helix; a disulfide bond; the egf-like 2 domain

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-asp132 (accessed [today's date]).

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