Is SBDS p.Val58fs (c.171dup) pathogenic?

SBDS p.Val58fs (c.171dup) is classified Likely pathogenic in SBDS (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-20). No gnomAD frequency available for this variant; Associated with aplastic anemia.

What condition is associated with SBDS p.Val58fs (c.171dup)?

SBDS p.Val58fs (c.171dup) is associated with aplastic anemia (ClinVar).

How common is SBDS p.Val58fs (c.171dup) in the general population?

SBDS p.Val58fs (c.171dup) is no gnomAD frequency available for this variant (gnomAD).

SBDS p.Val58fs

c.171dup · rs2536930168 · VCV3240426

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

aplastic anemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 5
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.8, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

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: SBDS
Protein: p.Val58fs
Coding: c.171dup
MANE Select: NM_016038
dbSNP: rs2536930168
Type: Duplication
Location: chr7:66994298 (GRCh38)
Gene constraint: LOEUF 1.08 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.97 · 6 PDB
Residue 58: a β-strand

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

Disease context

aplastic anemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SBDS p.Val58Ala Uncertain significance ★★ ⚠ same residue
SBDS p.Gln152fs Likely pathogenic ★★ same condition
SBDS p.His54fs Pathogenic ★ same condition
SBDS p.Trp39fs Likely pathogenic ★ same condition
SBDS c.258+1G>C Pathogenic ★★ same condition
SBDS c.258+2T>C Pathogenic/Likely pathogenic ★★ same condition
SBDS c.624+1G>A Likely pathogenic ★★ same condition
SBDS p.Arg218Gln Pathogenic/Likely pathogenic ★★ ⚠ 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/sbds-p-val58fs (accessed [today's date]).

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