Is SRPX2 p.Ser367fs (c.1099del) pathogenic?

SRPX2 p.Ser367fs (c.1099del) is classified Uncertain significance in SRPX2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-11-19). No gnomAD frequency available for this variant.

How common is SRPX2 p.Ser367fs (c.1099del) in the general population?

SRPX2 p.Ser367fs (c.1099del) is no gnomAD frequency available for this variant (gnomAD).

SRPX2 p.Ser367fs

c.1099del · rs1556013967 · VCV504185

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	predicted	premature termination codon in exon 10 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.2	GERP 1.9, 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: SRPX2
Protein: p.Ser367fs
Coding: c.1099del
MANE Select: NM_014467
dbSNP: rs1556013967
Type: Deletion
Location: chrX:100669251 (GRCh38)
Structure: AlphaFold pLDDT 86.75

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

Similar variants

SRPX2 p.Leu13fs Uncertain significance ★ same type
SRPX2 c.164-217del Benign ★ same type
SRPX2 c.164-218_164-217del Likely benign ★ same type
SRPX2 c.659+8_659+22del Likely benign ★ same type
SRPX2 c.660-16del 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/srpx2-p-ser367fs (accessed [today's date]).

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