Is BFSP1 p.Ile313= (c.939C>T) pathogenic?

BFSP1 p.Ile313= (c.939C>T) is classified Likely benign in BFSP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-04-22). Rare (popmax 0.247%, afr); Associated with BFSP1-related disorder.

What condition is associated with BFSP1 p.Ile313= (c.939C>T)?

BFSP1 p.Ile313= (c.939C>T) is associated with BFSP1-related disorder (ClinVar).

How common is BFSP1 p.Ile313= (c.939C>T) in the general population?

BFSP1 p.Ile313= (c.939C>T) is rare (popmax 0.247%, afr) (gnomAD).

BFSP1 p.Ile313=

c.939C>T · VCV3354128

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.247%, afr)

Conditions

BFSP1-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.4	GERP -4.2
Overall
CADD	1.775	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.247% African / African-American · 185/75,006 alleles

Filtering AF 0.218% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.206%

Overall 0.0137% 221/1,612,970 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.247%	405
Admixed American	0.0267%	3,750
Remaining individualsnot grpmax-eligible	0.0112%	8,913
East Asian	0.00669%	14,958
South Asian	0.0022%	45,504
European (non-Finnish)	0.000678%	147,498

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: BFSP1
Protein: p.Ile313=
Coding: c.939C>T
MANE Select: NM_001195
Type: single nucleotide variant
Location: chr20:17498837 (GRCh38)
Gene constraint: LOEUF 1.371 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.66
Residue 313: the if rod domain; the 'coil 2' region

Full BFSP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

BFSP1-related disorder

Similar variants

BFSP1 p.Gly384Val Uncertain significance ⚠ same condition
BFSP1 p.Val480Met Uncertain significance ⚠ same condition
BFSP1 c.1042+5C>T Likely benign same condition
BFSP1 p.Leu156= Likely benign same condition
BFSP1 p.Ala643Thr Uncertain significance ★★ ⚠ same type
BFSP1 p.Arg560Cys Uncertain significance ★★ ⚠ same type
BFSP1 p.Arg69Trp Uncertain significance ★★ ⚠ same type
BFSP1 p.Asp19Asn Uncertain significance ★★ ⚠ same type

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/bfsp1-p-ile313 (accessed [today's date]).

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