Is F7 p.Arg262Gln (c.785G>A) pathogenic?

F7 p.Arg262Gln (c.785G>A) is classified Conflicting classifications of pathogenicity in F7 (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2024-05-13). AlphaMissense: likely benign (0.0764); Rare (popmax 0.272%, afr); Associated with congenital factor VII deficiency.

What condition is associated with F7 p.Arg262Gln (c.785G>A)?

F7 p.Arg262Gln (c.785G>A) is associated with congenital factor VII deficiency, factor VII deficiency (ClinVar).

How common is F7 p.Arg262Gln (c.785G>A) in the general population?

F7 p.Arg262Gln (c.785G>A) is rare (popmax 0.272%, afr) (gnomAD).

How is Congenital factor VII deficiency inherited?

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

What do computational predictors say about F7 p.Arg262Gln (c.785G>A)?

AlphaMissense predicts likely benign (score 0.0764) — an in-silico prediction, not a clinical call.

F7 p.Arg262Gln

c.785G>A · rs77121822 · VCV734839

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.0764 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.272%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

congenital factor VII deficiency

Computational evidence

Protein change
AlphaMissense	0.0764	likely benign
REVEL	0.096	moderately benign-leaning
SaProt	LLR -5.53	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.6	GERP -3.1
Regional constraint	o/e 0.95	unconstrained · MANE · 13 kb · p 0.22 · regional, not allelic
Overall
CADD	0.031	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R284Q vs ClinVar R262Q) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.272% African / African-American · 204/74,982 alleles

Filtering AF 0.242% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.23%

Overall 0.0439% 705/1,606,384 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.272%	368
Middle Eastern	0.165%	605
Remaining individualsnot grpmax-eligible	0.101%	988
Admixed American	0.0851%	1,175
East Asian	0.0313%	3,199
European (non-Finnish)	0.0301%	3,327
South Asian	0.0099%	10,102

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: F7
Protein: p.Arg262Gln
Coding: c.785G>A
MANE Select: NM_019616
dbSNP: rs77121822
Type: single nucleotide variant
Location: chr13:113118458 (GRCh38)
Gene constraint: LOEUF 1.113 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 82.64 · 114 PDB
Residue 262: an α-helix; a disulfide bond; the peptidase s1 domain

Full F7 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Also linked: factor VII deficiency

For Congenital factor VII deficiency (Orphanet):

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

Similar variants

F7 p.Arg262fs Pathogenic same residue
F7 p.Arg262Trp Uncertain significance ★ ⚠ same residue
F7 c.225+1G>C Pathogenic ★★ same condition
F7 c.364+1G>A Pathogenic/Likely pathogenic ★★ same condition
F7 c.505+78G>A Pathogenic/Likely pathogenic ★★ same condition
F7 c.615+1G>T Pathogenic/Likely pathogenic ★★ same condition
F7 c.739+1G>A Pathogenic/Likely pathogenic ★★ same condition
F7 c.-30A>C Likely 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/f7-p-arg262gln (accessed [today's date]).

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