Is BNC1 p.Phe207fs (c.621_637del) pathogenic?

BNC1 p.Phe207fs (c.621637del) is classified Likely pathogenic in BNC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-09-01). Absent from gnomAD; Associated with Male infertility with azoospermia or oligozoospermia due to single gene mutation.

What condition is associated with BNC1 p.Phe207fs (c.621_637del)?

BNC1 p.Phe207fs (c.621_637del) is associated with Male infertility with azoospermia or oligozoospermia due to single gene mutation (ClinVar).

How common is BNC1 p.Phe207fs (c.621_637del) in the general population?

BNC1 p.Phe207fs (c.621_637del) is absent from gnomAD (gnomAD).

BNC1 p.Phe207fs

c.621_637del · rs2547958432 · VCV2690982

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Male infertility with azoospermia or oligozoospermia due to single gene mutation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 4 of 5
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.3	GERP -0.099, phastCons 0.091

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BNC1
Protein: p.Phe207fs
Coding: c.621_637del
MANE Select: NM_001717
dbSNP: rs2547958432
Type: Deletion
Location: chr15:83264614 (GRCh38)
Gene constraint: LOEUF 0.212 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 54.85

Full BNC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Male infertility with azoospermia or oligozoospermia due to single gene mutation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BNC1 p.Pro625fs Likely pathogenic ★ same condition
BNC1 p.Ser45fs Uncertain significance ★ same type
BNC1 p.Arg356fs Pathogenic 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/bnc1-p-phe207fs (accessed [today's date]).

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