Is WRAP53 p.Ser491fs (c.1471_1472del) pathogenic?

WRAP53 p.Ser491fs (c.14711472del) is classified Uncertain significance in WRAP53 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-03-25). No gnomAD frequency available for this variant.

How common is WRAP53 p.Ser491fs (c.1471_1472del) in the general population?

WRAP53 p.Ser491fs (c.1471_1472del) is no gnomAD frequency available for this variant (gnomAD).

WRAP53 p.Ser491fs

c.1471_1472del · rs2151097650 · VCV1381712

Uncertain significance Single submitter

Classification

Uncertain significance

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	escapes	premature termination codon in the last exon (11 of 11) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.23	GERP -0.55

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: WRAP53
Protein: p.Ser491fs
Coding: c.1471_1472del
MANE Select: NM_001143992
dbSNP: rs2151097650
Type: Microsatellite
Location: chr17:7703306 (GRCh38)
Gene constraint: LOEUF 0.645 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 73.96 · 7 PDB
Residue 491: a modified residue (phosphoserine)

Full WRAP53 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

WRAP53 p.Leu75fs Uncertain significance ★★ same type
WRAP53 p.Glu117del Uncertain significance ★ same type
WRAP53 p.Phe485fs Uncertain significance ★ same type
WRAP53 p.Ser438fs Uncertain significance ★ same type
WRAP53 c.1269-13CT[3] Likely benign ★ same type
WRAP53 c.1269-19TC[2] Likely benign ★ 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/wrap53-p-ser491fs (accessed [today's date]).

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