SPEM2
protein-codingSPEM family member 2
Gene summary
Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]
- C17orf74
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.0 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 SPEM2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_175734.5. 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 | 0 | |||||
| missense | 8 | 8 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 | 8 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_783861.3 | 3 | MANE Select | |
| Ensembl | ENSP00000328061.3 | 3 | MANE Select | |
| Ensembl | ENSP00000458799.1 | 3 | Standard | |
| Ensembl | ENSP00000458799.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000333870
- Coding exons
- 3
- Length
- 1954
- Individuals with no LoFs
- 124754
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 50
- Defined
- 124804
- p
- 0.000200
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0691 | 342 | 338 | 1.01 | 0.0000232 | 3236 |
| Missense (PolyPhen) | 99 | 89.743 | 1.1031 | 804 | ||
| Synonymous | 0.920 | 117 | 130 | 0.897 | 0.00000794 | 1064 |
| Loss of Function | 0.320 | 18 | 19.5 | 0.922 | 0.00000111 | 177 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00028 | 0.00028 | rare |
| Finnish | 0.00019 | 0.00019 | rare |
| European (Non-Finnish) | 0.00020 | 0.00019 | rare |
| South Asian | 0.00033 | 0.00033 | rare |
| Other | 0.00050 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- 0.67
- RVIS percentile EVS
- 84.68
Essentials
- Essential (gene trap)
- N