Is BFSP2 p.Arg318Ser (c.954G>T) pathogenic?

BFSP2 p.Arg318Ser (c.954G>T) is classified Likely benign in BFSP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-03). AlphaMissense: likely benign (0.2028); Rare (popmax 0.566%, afr); Associated with cataract 12 multiple types.

What condition is associated with BFSP2 p.Arg318Ser (c.954G>T)?

BFSP2 p.Arg318Ser (c.954G>T) is associated with cataract 12 multiple types (ClinVar).

How common is BFSP2 p.Arg318Ser (c.954G>T) in the general population?

BFSP2 p.Arg318Ser (c.954G>T) is rare (popmax 0.566%, afr) (gnomAD).

What do computational predictors say about BFSP2 p.Arg318Ser (c.954G>T)?

AlphaMissense predicts likely benign (score 0.2028) — an in-silico prediction, not a clinical call.

BFSP2 p.Arg318Ser

c.954G>T · rs146972354 · VCV474094

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2028 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.566%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

cataract 12 multiple types

Computational evidence

Protein change
AlphaMissense	0.2028	likely benign
REVEL	0.426	indeterminate
SaProt	LLR -7.76	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL is indeterminate.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.35	GERP -3.6, phastCons 0.11
Regional constraint	o/e 0.99	unconstrained · MANE · 75 kb · p 0.73 · regional, not allelic
Overall
CADD	14.88	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 0.566% African / African-American · 424/74,976 alleles

Filtering AF 0.521% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.504%

Overall 0.0312% 504/1,613,946 alleles · rare exomes 241/1,461,818 · genomes 263/152,128 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.566%	177
Admixed American	0.0767%	1,304
Remaining individualsnot grpmax-eligible	0.0464%	2,155
South Asian	0.0011%	91,064
European (non-Finnish)	0.000339%	294,992

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: BFSP2
Protein: p.Arg318Ser
Coding: c.954G>T
MANE Select: NM_003571
dbSNP: rs146972354
Type: single nucleotide variant
Location: chr3:133466890 (GRCh38)
Gene constraint: LOEUF 1.067 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.15
Residue 318: the if rod domain

Full BFSP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cataract 12 multiple types — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BFSP2 p.Arg4Lys Uncertain significance ★★ ⚠ same condition
BFSP2 p.Arg5Ter Uncertain significance ★★ same condition
BFSP2 p.Arg72His Uncertain significance ★★ ⚠ same condition
BFSP2 p.Glu141Ala Uncertain significance ★★ ⚠ same condition
BFSP2 p.Glu289Asp Uncertain significance ★★ ⚠ same condition
BFSP2 p.Leu153Gln Uncertain significance ★★ ⚠ same condition
BFSP2 c.572+160A>G Benign ★★ same condition
BFSP2 c.730-7T>C Benign/Likely benign ★★ 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/bfsp2-p-arg318ser (accessed [today's date]).

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