Is F5 p.Gln79= (c.237A>G) pathogenic?

F5 p.Gln79= (c.237A>G) is classified Benign/Likely benign in F5 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-02-04). Common (popmax 39.1%, amr) — too common for a highly-penetrant pathogenic allele; Associated with congenital factor V deficiency.

What condition is associated with F5 p.Gln79= (c.237A>G)?

F5 p.Gln79= (c.237A>G) is associated with congenital factor V deficiency, thrombophilia due to thrombin defect, Budd-Chiari syndrome (ClinVar).

How is Congenital factor V deficiency inherited?

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

F5 p.Gln79=

Q: How common is F5 p.Gln79= (c.237A>G) in the general population?

F5 p.Gln79= (c.237A>G) is common (popmax 39.1%, amr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.237A>G · rs6028 · VCV255197

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Common

common (popmax 39.1%, amr) — too common for a highly-penetrant pathogenic allele

Conditions

congenital factor V 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 0.14	GERP -0.46
Overall
CADD	5.539	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 39.1% Admixed American · 22,496/57,566 alleles

Filtering AF 38.7% ClinGen BA1/BS1 input FAF95, joint · FAF99 38.5%

Overall 27.1% 408,412/1,507,572 alleles · common

Ancestry group	Frequency	1 in
Admixed Americangrpmax	39.1%	3
Finnishnot grpmax-eligible	34.2%	3
South Asian	33.6%	3
European (non-Finnish)	27.2%	4
Ashkenazi Jewishnot grpmax-eligible	25.8%	4
Remaining individualsnot grpmax-eligible	25.4%	4
East Asian	25.1%	4
Middle Eastern	20.8%	5
Amishnot grpmax-eligible	15.3%	7
African / African-American	6.18%	16

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: F5
Protein: p.Gln79=
Coding: c.237A>G
MANE Select: NM_000130
dbSNP: rs6028
Type: single nucleotide variant
Location: chr1:169582444 (GRCh38)
Gene constraint: LOEUF 0.704 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.57 · 23 PDB
Residue 79: an α-helix; the f5/8 type a 1 domain; the plastocyanin-like 1 domain

Full F5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Also linked: thrombophilia due to thrombin defect Budd-Chiari syndrome factor V deficiency

For Congenital factor V deficiency (Orphanet):

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

Similar variants

F5 c.1297-2A>G Pathogenic/Likely pathogenic ★★ same condition
F5 p.Arg1030Ter Pathogenic ★★ same condition
F5 p.Arg146Ter Pathogenic/Likely pathogenic ★★ same condition
F5 p.Arg1621Ter Pathogenic/Likely pathogenic ★★ same condition
F5 p.Arg1634Ter Pathogenic/Likely pathogenic ★★ same condition
F5 p.Arg2102His Pathogenic/Likely pathogenic ★★ same condition
F5 p.Arg740Ter Pathogenic/Likely pathogenic ★★ same condition
F5 p.Asp96His 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/f5-p-gln79 (accessed [today's date]).

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