Is APRT p.Val154fs (c.461_462del) pathogenic?

APRT p.Val154fs (c.461462del) is classified Pathogenic in APRT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-09-01). Absent from gnomAD; Associated with adenine phosphoribosyltransferase deficiency.

What condition is associated with APRT p.Val154fs (c.461_462del)?

APRT p.Val154fs (c.461_462del) is associated with adenine phosphoribosyltransferase deficiency (ClinVar).

How common is APRT p.Val154fs (c.461_462del) in the general population?

APRT p.Val154fs (c.461_462del) is absent from gnomAD (gnomAD).

How is Adenine phosphoribosyltransferase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

APRT p.Val154fs

c.461_462del · rs1909038050 · VCV988067

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

adenine phosphoribosyltransferase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (5 of 5) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.1	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: APRT
Protein: p.Val154fs
Coding: c.461_462del
MANE Select: NM_000485
dbSNP: rs1909038050
Type: Deletion
Location: chr16:88809779 (GRCh38)
Gene constraint: LOEUF 1.789 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.91 · 16 PDB
Residue 154: a β-strand

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

Disease context

adenine phosphoribosyltransferase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Adenine phosphoribosyltransferase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Elderly, Infancy
Prevalence: 1-9 / 100 000 (Specific population)

Similar variants

APRT p.Val154Met Uncertain significance ★★ ⚠ same residue
APRT p.Thr96fs Pathogenic/Likely pathogenic ★★ same condition
APRT c.401-40_401-25del Likely pathogenic ★ same condition
APRT p.Glu158del Pathogenic ★ same condition
APRT p.Glu5fs Likely pathogenic ★ same condition
APRT p.Phe39fs Likely pathogenic ★ same condition
APRT p.Ser175del Pathogenic ★ same condition
APRT p.Val154Glu Uncertain significance ★ ⚠ same residue

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/aprt-p-val154fs (accessed [today's date]).

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