Is BFSP1 p.Ala38Val (c.113C>T) pathogenic?

BFSP1 p.Ala38Val (c.113C>T) is classified Uncertain significance in BFSP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-29). AlphaMissense: likely benign (0.1151); Very rare (popmax 0.00318%, eas); Associated with Inborn genetic diseases.

What condition is associated with BFSP1 p.Ala38Val (c.113C>T)?

BFSP1 p.Ala38Val (c.113C>T) is associated with Inborn genetic diseases (ClinVar).

How common is BFSP1 p.Ala38Val (c.113C>T) in the general population?

BFSP1 p.Ala38Val (c.113C>T) is very rare (popmax 0.00318%, eas) (gnomAD).

What do computational predictors say about BFSP1 p.Ala38Val (c.113C>T)?

AlphaMissense predicts likely benign (score 0.1151) — an in-silico prediction, not a clinical call.

BFSP1 p.Ala38Val

c.113C>T · VCV4206561

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1151 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00318%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1151	likely benign
REVEL	0.23	benign-leaning
SaProt	LLR -7.82	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.4	GERP -0.79, phastCons 0.037
Regional constraint	o/e 0.97	unconstrained · MANE · 37 kb · p 0.4 · regional, not allelic
Overall
CADD	15.63	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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

Grpmax group 0.00318% East Asian · 1/31,472 alleles

Overall 0.000225% 3/1,332,272 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00318%	31,472
South Asian	0.00188%	53,052
European (non-Finnish)	9.59e-05%	1,042,385

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.Ala38Val
Coding: c.113C>T
MANE Select: NM_001195
Type: single nucleotide variant
Location: chr20:17531217 (GRCh38)
Gene constraint: LOEUF 1.371 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.66
Residue 38: the 'head' region

Full BFSP1 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

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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-ala38val (accessed [today's date]).

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