Is F10 p.Ser93Asn (c.278G>A) pathogenic?

F10 p.Ser93Asn (c.278G>A) is classified Likely benign in F10 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-29). AlphaMissense: likely benign (0.0649); Very rare (popmax 0.00144%, nfe); Associated with Inborn genetic diseases.

What condition is associated with F10 p.Ser93Asn (c.278G>A)?

F10 p.Ser93Asn (c.278G>A) is associated with Inborn genetic diseases (ClinVar).

How common is F10 p.Ser93Asn (c.278G>A) in the general population?

F10 p.Ser93Asn (c.278G>A) is very rare (popmax 0.00144%, nfe) (gnomAD).

What do computational predictors say about F10 p.Ser93Asn (c.278G>A)?

AlphaMissense predicts likely benign (score 0.0649) — an in-silico prediction, not a clinical call.

F10 p.Ser93Asn

c.278G>A · VCV4020664

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0649 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00144%, nfe)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0649	likely benign
REVEL	0.297	indeterminate
SaProt	LLR -5.56	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -9.5	GERP -3.5
Regional constraint	o/e 1.08	unconstrained · MANE · 17 kb · p 0.36 · regional, not allelic
Overall
CADD	0.001	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00144% European (non-Finnish) · 17/1,179,874 alleles

Filtering AF 0.000878% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000718%

Overall 0.00105% 17/1,613,810 alleles · very rare

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.Ser93Asn
Coding: c.278G>A
MANE Select: NM_000504
Type: single nucleotide variant
Location: chr13:113139378 (GRCh38)
Gene constraint: LOEUF 0.968 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.47 · 192 PDB
Residue 93: a disulfide bond; the egf-like 1; calcium-binding domain

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

F10 p.Ser93Arg Uncertain significance ★ ⚠ same residue
F10 p.Glu268Lys Uncertain significance ★★ ⚠ same condition
F10 p.Ala185Asp Uncertain significance ★ ⚠ same condition
F10 p.Ala250Val Uncertain significance ★ same condition
F10 p.Ala457Thr Uncertain significance ★ ⚠ same condition
F10 p.Arg180Gly Uncertain significance ★ ⚠ same condition
F10 p.Arg28Thr Uncertain significance ★ ⚠ same condition
F10 p.Asn97Lys 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-ser93asn (accessed [today's date]).

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