SRPX
protein-codingsushi repeat containing protein X-linked, the group of Sushi domain containing
Gene summary
Predicted to be an extracellular matrix structural constituent. Predicted to be involved in phagolysosome assembly. Predicted to act upstream of or within several processes, including negative regulation of cell proliferation involved in contact inhibition; positive regulation of extrinsic apoptotic signaling pathway in absence of ligand; and response to endoplasmic reticulum stress. Located in extracellular matrix. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~71.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SRPX variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006307.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 3 | 1 | 7 | ||
| missense | 1 | 78 | 3 | 1 | 83 | |
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 1 | 91 | 6 | 2 | 100 |
Highest pathogenic variant AF is 0.000043913795
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006298.1 | 10 | MANE Select | |
| Ensembl | ENSP00000367794.3 | 10 | MANE Select | |
| RefSeq | NP_001164221.1 | 9 | Standard | |
| RefSeq | NP_001164222.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- phagolysosome assembly
- autophagy
- cell adhesion
- response to endoplasmic reticulum stress
- negative regulation of cell proliferation involved in contact inhibition
Molecular Function
- protein binding
Cellular Component
- autophagosome
- endoplasmic reticulum
- cell surface
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000378533
- Coding exons
- 10
- Length
- 72108
- Individuals with no LoFs
- 125725
- Homozygous LoFs
- 9
- Heterozygous LoFs
- 5
- Defined
- 125739
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.617 | 202 | 179 | 1.13 | 0.0000144 | 2960 |
| Missense (PolyPhen) | 84 | 80.878 | 1.0386 | 1381 | ||
| Synonymous | -0.168 | 75 | 73.2 | 1.02 | 0.00000608 | 961 |
| Loss of Function | 2.25 | 7 | 17.0 | 0.412 | 0.00000152 | 274 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000076 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00014 | 0.000088 | rare |
| South Asian | 0.00017 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in phagocytosis during disk shedding, cell adhesion to cells other than the pigment epithelium or signal transduction.;
Recessive Scores
- pRec
- 0.136
Intolerance Scores
- LoFtool
- 0.882
- RVIS EVS
- 0.22
- RVIS percentile EVS
- 68.38
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |