Is PEX6 p.Val359fs (c.1071_1072del) pathogenic?

PEX6 p.Val359fs (c.10711072del) is classified Pathogenic in PEX6 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-06-14). No gnomAD frequency available for this variant.

How common is PEX6 p.Val359fs (c.1071_1072del) in the general population?

PEX6 p.Val359fs (c.1071_1072del) is no gnomAD frequency available for this variant (gnomAD).

PEX6 p.Val359fs

c.1071_1072del · rs2481251681 · VCV2664540

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

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 3 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.9	GERP 1.8, 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: PEX6
Protein: p.Val359fs
Coding: c.1071_1072del
MANE Select: NM_000287
dbSNP: rs2481251681
Type: Deletion
Location: chr6:42974061 (GRCh38)
Gene constraint: LOEUF 0.799 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 69.87

Full PEX6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

PEX6 p.Val359Leu Uncertain significance ★ ⚠ same residue
PEX6 c.1368-2del Likely pathogenic ★★ same type
PEX6 p.Arg343fs Pathogenic/Likely pathogenic ★★ same type
PEX6 p.Asn233fs Pathogenic/Likely pathogenic ★★ same type
PEX6 p.Asp268fs Pathogenic ★★ same type
PEX6 p.Asp305fs Pathogenic/Likely pathogenic ★★ same type
PEX6 p.Cys564fs Pathogenic/Likely pathogenic ★★ same type
PEX6 p.Glu304fs Pathogenic/Likely 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/pex6-p-val359fs (accessed [today's date]).

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