Is SRPX2 p.Arg161Pro (c.482G>C) pathogenic?

SRPX2 p.Arg161Pro (c.482G>C) is classified Uncertain significance in SRPX2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-22). AlphaMissense: likely pathogenic (0.9979); Absent from gnomAD v4.1.

How common is SRPX2 p.Arg161Pro (c.482G>C) in the general population?

SRPX2 p.Arg161Pro (c.482G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about SRPX2 p.Arg161Pro (c.482G>C)?

AlphaMissense predicts likely pathogenic (score 0.9979) — an in-silico prediction, not a clinical call.

SRPX2 p.Arg161Pro

c.482G>C · VCV3449486

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9979 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.9979	likely pathogenic · top 2% in SRPX2
REVEL	0.603	indeterminate
SaProt	LLR -12.65	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 25 kb · p 0.025 · regional, not allelic
Overall
CADD	29.8	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

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.Arg161Pro
Coding: c.482G>C
MANE Select: NM_014467
Type: single nucleotide variant
Location: chrX:100664900 (GRCh38)
Structure: AlphaFold pLDDT 86.75
Residue 161: the sushi 2 domain

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

Similar variants

SRPX2 p.Arg161= Benign/Likely benign ★★ same residue
SRPX2 p.Arg161Gln Uncertain significance ★ same residue
SRPX2 c.961+1G>A Uncertain significance ★★ same type
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
SRPX2 p.Arg430His 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-arg161pro (accessed [today's date]).

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