MS4A6A
protein-codingmembrane spanning 4-domains A6A, the group of Membrane spanning 4-domains
Gene summary
This gene encodes a member of the membrane-spanning 4A gene family. Members of this nascent protein family are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns among hematopoietic cells and nonlymphoid tissues. The gene encoding this protein is localized to 11q12.1, among a cluster of family members. Alternative splicing of this gene results in several transcript variants that encode different protein isoforms. [provided by RefSeq, Oct 2011]
- MS4A6
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~13.1 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 MS4A6A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022349.4. 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 | 1 | 4 | |||
| missense | 18 | 5 | 23 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 22 | 6 | 0 | 28 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071744.2 | 5 | MANE Select | |
| Ensembl | ENSP00000431901.1 | 5 | MANE Select | |
| RefSeq | NP_001234928.1 | 6 | Standard | |
| RefSeq | NP_001317204.1 | 7 | 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
- ENST00000412309
- Coding exons
- 6
- Length
- 13059
- Individuals with no LoFs
- 125279
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 463
- Defined
- 125744
- p
- 0.00185
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.457 | 144 | 129 | 1.11 | 0.00000609 | 1625 |
| Missense (PolyPhen) | 35 | 30.948 | 1.1309 | 440 | ||
| Synonymous | -0.381 | 56 | 52.5 | 1.07 | 0.00000260 | 528 |
| Loss of Function | -1.84 | 15 | 9.04 | 1.66 | 3.78e-7 | 125 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00075 | 0.00075 | rare |
| Ashkenazi Jewish | 0.00069 | 0.00069 | rare |
| East Asian | 0.0030 | 0.0030 | notable |
| Finnish | 0.0043 | 0.0043 | notable |
| European (Non-Finnish) | 0.0023 | 0.0023 | notable |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.0020 | 0.0020 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in signal transduction as a component of a multimeric receptor complex.;
Recessive Scores
- pRec
- 0.0823
Intolerance Scores
- LoFtool
- 0.946
- RVIS EVS
- 0.48
- RVIS percentile EVS
- 79.25
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.00858
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |