Is SRPX2 p.Arg393= (c.1179G>A) pathogenic?

SRPX2 p.Arg393= (c.1179G>A) is classified Likely benign in SRPX2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-01-03). Absent from gnomAD v4.1; Associated with SRPX2-related disorder.

What condition is associated with SRPX2 p.Arg393= (c.1179G>A)?

SRPX2 p.Arg393= (c.1179G>A) is associated with SRPX2-related disorder (ClinVar).

How common is SRPX2 p.Arg393= (c.1179G>A) in the general population?

SRPX2 p.Arg393= (c.1179G>A) is absent from gnomAD v4.1 (gnomAD).

SRPX2 p.Arg393=

c.1179G>A · rs2520312647 · VCV3033945

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

SRPX2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 1.5	GERP -1.1, phastCons 1
Overall
CADD	9.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: SRPX2
Protein: p.Arg393=
Coding: c.1179G>A
MANE Select: NM_014467
dbSNP: rs2520312647
Type: single nucleotide variant
Location: chrX:100669331 (GRCh38)
Structure: AlphaFold pLDDT 86.75

Full SRPX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

SRPX2-related disorder

Similar variants

SRPX2 p.Arg393Gln Uncertain significance ★ ⚠ same residue
SRPX2 p.Arg393Trp Uncertain significance ★ ⚠ same residue
SRPX2 c.961+1G>A Uncertain significance ★★ same condition
SRPX2 p.Gly295Arg Uncertain significance ★ ⚠ same condition
SRPX2 p.Ala201Val Uncertain significance ★★ ⚠ same type
SRPX2 p.Arg185Cys Uncertain significance ★★ ⚠ same type
SRPX2 p.Arg185Leu Uncertain significance ★★ ⚠ same type
SRPX2 p.Arg413His Uncertain significance ★★ ⚠ 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/srpx2-p-arg393 (accessed [today's date]).

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