Is F13B p.Pro386fs (c.1152_1155dup) pathogenic?

F13B p.Pro386fs (c.11521155dup) is classified Pathogenic in F13B (ClinVar, Single submitter, 1 submitter; last evaluated 2020-05-26). Ultra-rare (popmax 0.0362%, sas); Associated with factor XIII, b subunit, deficiency of.

What condition is associated with F13B p.Pro386fs (c.1152_1155dup)?

F13B p.Pro386fs (c.1152_1155dup) is associated with factor XIII, b subunit, deficiency of (ClinVar).

How common is F13B p.Pro386fs (c.1152_1155dup) in the general population?

F13B p.Pro386fs (c.1152_1155dup) is ultra-rare (popmax 0.0362%, sas) (gnomAD).

How is Congenital factor XIII deficiency inherited?

Typically Autosomal recessive, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

F13B p.Pro386fs

c.1152_1155dup · rs748757906 · VCV1698968

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

ultra-rare (popmax 0.0362%, sas)

Conditions

factor XIII, b subunit, deficiency of

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 7 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.4	GERP -0.001, phastCons 0.84

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0362% South Asian · 33/91,084 alleles

Filtering AF 0.0265% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0231%

Overall 0.00236% 38/1,613,548 alleles · ultra-rare exomes 38/1,461,234 · genomes 0/152,314 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0362%	2,760
Remaining individualsnot grpmax-eligible	0.008%	12,497

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: F13B
Protein: p.Pro386fs
Coding: c.1152_1155dup
MANE Select: NM_001994
dbSNP: rs748757906
Type: Duplication
Location: chr1:197057028 (GRCh38)
Gene constraint: LOEUF 0.893 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 80.55 · 2 PDB
Residue 386: the sushi 6 domain

Full F13B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

factor XIII, b subunit, deficiency of — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Congenital factor XIII deficiency (Orphanet):

Inheritance: Autosomal recessive, Not applicable
Onset: All ages
Prevalence: <1 / 1 000 000 (Europe)

Similar variants

F13B p.Cys59fs Likely pathogenic ★ same condition
F13B c.805+1G>A Likely pathogenic ★★ same condition
F13B p.Tyr100Ter Pathogenic ★★ same condition
F13B c.986-4T>C Uncertain significance ★★ same condition
F13B p.Ala363= Uncertain significance ★★ same condition
F13B p.Arg293Cys Uncertain significance ★★ ⚠ same condition
F13B p.Arg645Ser Uncertain significance ★★ ⚠ same condition
F13B p.His225Gln 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/f13b-p-pro386fs (accessed [today's date]).

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