Is BFSP2 p.Asn240= (c.720C>T) pathogenic?

BFSP2 p.Asn240= (c.720C>T) is classified Benign in BFSP2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2020-10-05). Rare (popmax 0.277%, sas); Associated with cataract 12 multiple types.

What condition is associated with BFSP2 p.Asn240= (c.720C>T)?

BFSP2 p.Asn240= (c.720C>T) is associated with cataract 12 multiple types (ClinVar).

How common is BFSP2 p.Asn240= (c.720C>T) in the general population?

BFSP2 p.Asn240= (c.720C>T) is rare (popmax 0.277%, sas) (gnomAD).

BFSP2 p.Asn240=

c.720C>T · rs376911067 · VCV903007

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.277%, sas)

Conditions

cataract 12 multiple types

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.44 · evaluated, not missing
Constraint at this position
Conservation	phyloP 2.6	GERP 1.9, phastCons 1
Overall
CADD	8.961	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.277% South Asian · 252/91,004 alleles

Filtering AF 0.249% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.238%

Overall 0.0432% 697/1,613,680 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.277%	361
Middle Eastern	0.201%	497
Remaining individualsnot grpmax-eligible	0.0672%	1,488
European (non-Finnish)	0.0306%	3,268
Admixed American	0.0267%	3,750
Ashkenazi Jewishnot grpmax-eligible	0.0237%	4,228
African / African-American	0.00933%	10,717

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.Asn240=
Coding: c.720C>T
MANE Select: NM_003571
dbSNP: rs376911067
Type: single nucleotide variant
Location: chr3:133448636 (GRCh38)
Gene constraint: LOEUF 1.067 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 78.15
Residue 240: 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-asn240 (accessed [today's date]).

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