Is ASPA p.Asp230fs (c.689_698del) pathogenic?

ASPA p.Asp230fs (c.689698del) is classified Likely pathogenic in ASPA (ClinVar, Single submitter, 1 submitter; last evaluated 2018-03-30). Absent from gnomAD.

How common is ASPA p.Asp230fs (c.689_698del) in the general population?

ASPA p.Asp230fs (c.689_698del) is absent from gnomAD (gnomAD).

ASPA p.Asp230fs

c.689_698del · rs1555540679 · VCV523964

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

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 5 of 6
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.2	GERP -1.5, phastCons 1

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: ASPA
Protein: p.Asp230fs
Coding: c.689_698del
MANE Select: NM_000049
dbSNP: rs1555540679
Type: Deletion
Location: chr17:3494403 (GRCh38)
Gene constraint: LOEUF 1.098 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 96.14 · 8 PDB
Residue 230: an α-helix

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

Similar variants

ASPA p.Asp204fs Pathogenic/Likely pathogenic ★★ same type
ASPA p.Cys152fs Pathogenic/Likely pathogenic ★★ same type
ASPA p.Cys276fs Pathogenic/Likely pathogenic ★★ same type
ASPA p.Gln12fs Pathogenic ★★ same type
ASPA p.Glu129fs Pathogenic ★★ same type
ASPA p.Ile11fs Pathogenic/Likely pathogenic ★★ same type
ASPA p.Lys103fs Likely pathogenic ★★ same type
ASPA p.Met82fs 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/aspa-p-asp230fs (accessed [today's date]).

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