SHISAL2A
protein-codingshisa like 2A
Gene summary
Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]
- FAM159A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~36.5 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 SHISAL2A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001042693.3. 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 | 34 | 3 | 37 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 34 | 3 | 0 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001036158.1 | 3 | MANE Select | |
| Ensembl | ENSP00000429726.1 | 3 | MANE Select | |
| Ensembl | ENSP00000660072.1 | 3 | Standard | |
| Ensembl | ENSP00000660073.1 | 2 | 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
- ENST00000517870
- Coding exons
- 3
- Length
- 36340
- Individuals with no LoFs
- 124779
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 22
- Defined
- 124801
- p
- 0.0000881
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.278 | 121 | 113 | 1.07 | 0.00000570 | 1248 |
| Missense (PolyPhen) | 52 | 46.096 | 1.1281 | 510 | ||
| Synonymous | -0.184 | 48 | 46.4 | 1.03 | 0.00000252 | 372 |
| Loss of Function | -0.345 | 6 | 5.16 | 1.16 | 2.20e-7 | 57 |
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 | 0.00050 | 0.00050 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000047 | 0.000044 | rare |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- -0.01
- RVIS percentile EVS
- 53.19
Essentials
- Essential (gene trap)
- N