Is PEX1 p.Ser102Pro (c.304T>C) pathogenic?

PEX1 p.Ser102Pro (c.304T>C) is classified Uncertain significance in PEX1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-03). AlphaMissense: likely benign (0.2202); No allele count reported in gnomAD v4.1 (AN 1,610,536); Associated with Inborn genetic diseases.

What condition is associated with PEX1 p.Ser102Pro (c.304T>C)?

PEX1 p.Ser102Pro (c.304T>C) is associated with Inborn genetic diseases (ClinVar).

How common is PEX1 p.Ser102Pro (c.304T>C) in the general population?

PEX1 p.Ser102Pro (c.304T>C) is no allele count reported in gnomAD v4.1 (AN 1,610,536) (gnomAD).

What do computational predictors say about PEX1 p.Ser102Pro (c.304T>C)?

AlphaMissense predicts likely benign (score 0.2202) — an in-silico prediction, not a clinical call.

PEX1 p.Ser102Pro

c.304T>C · VCV3417074

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2202 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,610,536)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2202	likely benign
REVEL	0.803	moderately pathogenic-leaning
SaProt	LLR -5.96	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.1, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 41 kb · p 4.3e-05 · regional, not allelic
Overall
CADD	25.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,610,536). 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: PEX1
Protein: p.Ser102Pro
Coding: c.304T>C
MANE Select: NM_000466
Type: single nucleotide variant
Location: chr7:92519048 (GRCh38)
Gene constraint: LOEUF 0.746 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.19

Full PEX1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PEX1 p.Ser102Tyr Uncertain significance ★★ ⚠ same residue
PEX1 p.Ser102fs Likely pathogenic ★★ same residue
PEX1 p.Ala272Thr Uncertain significance ★★ ⚠ same condition
PEX1 p.Arg633Gln Uncertain significance ★★ ⚠ same condition
PEX1 p.Asp1168Asn Uncertain significance ★★ ⚠ same condition
PEX1 p.Asp417Asn Uncertain significance ★★ ⚠ same condition
PEX1 p.Gln448Leu Uncertain significance ★★ ⚠ same condition
PEX1 p.Gln582His Uncertain significance ★★ ⚠ 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/pex1-p-ser102pro (accessed [today's date]).

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