PACC1
protein-codingproton activated chloride channel 1
Gene summary
Enables pH-gated chloride channel activity. Involved in chloride transport. Located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]
- C1orf75
- TMEM206
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~51.0 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 PACC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018252.3. 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 | 4 | 4 | ||||
| missense | 59 | 2 | 61 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 63 | 2 | 0 | 65 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060722.2 | 8 | MANE Select | |
| Ensembl | ENSP00000261455.4 | 8 | MANE Select | |
| RefSeq | NP_001185791.1 | 9 | Standard | |
| RefSeq | NP_001364407.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Cellular Component
- cell surface
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000535273
- Coding exons
- 9
- Length
- 50971
- Individuals with no LoFs
- 125109
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 637
- Defined
- 125748
- p
- 0.00254
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.450 | 215 | 234 | 0.917 | 0.0000134 | 2687 |
| Missense (PolyPhen) | 89 | 99.831 | 0.8915 | 1196 | ||
| Synonymous | 0.448 | 85 | 90.4 | 0.940 | 0.00000527 | 802 |
| Loss of Function | 0.652 | 16 | 19.1 | 0.839 | 8.13e-7 | 229 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00086 | 0.00086 | rare |
| Latino/Admixed American | 0.0038 | 0.0038 | notable |
| Ashkenazi Jewish | 0.00089 | 0.00089 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00074 | 0.00074 | rare |
| European (Non-Finnish) | 0.0038 | 0.0038 | notable |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.0051 | 0.0051 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.367
- RVIS EVS
- -0.45
- RVIS percentile EVS
- 24.19
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.519
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |