Is FAR1 p.Ser84Arg (c.250A>C) pathogenic?

FAR1 p.Ser84Arg (c.250A>C) is classified Uncertain significance in FAR1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-12-06). AlphaMissense: likely pathogenic (0.9814); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with FAR1 p.Ser84Arg (c.250A>C)?

FAR1 p.Ser84Arg (c.250A>C) is associated with Inborn genetic diseases (ClinVar).

How common is FAR1 p.Ser84Arg (c.250A>C) in the general population?

FAR1 p.Ser84Arg (c.250A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about FAR1 p.Ser84Arg (c.250A>C)?

AlphaMissense predicts likely pathogenic (score 0.9814) — an in-silico prediction, not a clinical call.

FAR1 p.Ser84Arg

c.250A>C · rs2500114174 · VCV2333757

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9814 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9814	likely pathogenic · top 5% in FAR1
REVEL	0.376	indeterminate
SaProt	LLR -13.63	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 11	GERP 2, phastCons 1
Regional constraint	o/e 0.60	unconstrained · MANE · 34 kb · p 2.6e-21 · regional, not allelic
Overall
CADD	26.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: FAR1
Protein: p.Ser84Arg
Coding: c.250A>C
MANE Select: NM_032228
dbSNP: rs2500114174
Type: single nucleotide variant
Location: chr11:13700377 (GRCh38)
Gene constraint: LOEUF 0.595 · pLI 0.57 (gnomAD)
Structure: AlphaFold pLDDT 94.13

Full FAR1 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

FAR1 p.Ser84= Likely benign ★★ same residue
FAR1 p.Arg160Cys Uncertain significance ★★ ⚠ same condition
FAR1 p.Arg160His Uncertain significance ★★ ⚠ same condition
FAR1 p.Arg336Lys Uncertain significance ★★ ⚠ same condition
FAR1 p.Arg337Gln Uncertain significance ★★ same condition
FAR1 p.Arg467His Uncertain significance ★★ ⚠ same condition
FAR1 p.Arg508Gln Uncertain significance ★★ same condition
FAR1 p.Asn270Ser 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/far1-p-ser84arg (accessed [today's date]).

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