SERPINA6
Basic information
Region (hg38): 14:94304247-94323389
Previous symbols: [ "CBG" ]
Links
Phenotypes
GenCC
Source:
- corticosteroid-binding globulin deficiency (Supportive), mode of inheritance: Semidominant
- corticosteroid-binding globulin deficiency (Strong), mode of inheritance: AR
- corticosteroid-binding globulin deficiency (Moderate), mode of inheritance: AD
- corticosteroid-binding globulin deficiency (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Corticosteroid-binding globulin deficiency | AD/AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Endocrine | 7061486; 8212073; 10634411; 11502797; 17245537; 20610591; 22013108; 22337907; 22948765 |
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (12 variants)
- not provided (5 variants)
- Corticosteroid-binding globulin deficiency (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERPINA6 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 1 | |||||
missense | 15 | 15 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 15 | 0 | 1 |
Variants in SERPINA6
This is a list of pathogenic ClinVar variants found in the SERPINA6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
14-94304457-C-G | Uncertain significance (Dec 09, 2022) | |||
14-94304471-C-T | Corticosteroid-binding globulin deficiency | Conflicting classifications of pathogenicity (Feb 26, 2022) | ||
14-94304490-G-C | SERPINA6-related disorder | Likely benign (Jun 25, 2019) | ||
14-94304498-T-G | Inborn genetic diseases | Uncertain significance (Oct 30, 2023) | ||
14-94304599-A-G | Inborn genetic diseases | Uncertain significance (Feb 17, 2024) | ||
14-94306092-G-A | SERPINA6-related disorder | Benign (Dec 07, 2023) | ||
14-94306093-T-C | Inborn genetic diseases | Uncertain significance (Dec 07, 2021) | ||
14-94306106-G-A | Inborn genetic diseases | Uncertain significance (Aug 28, 2023) | ||
14-94306167-G-A | SERPINA6-related disorder | Benign (Nov 12, 2019) | ||
14-94306224-C-T | SERPINA6-related disorder | Likely benign (Mar 02, 2019) | ||
14-94309773-C-G | Uncertain significance (Aug 17, 2022) | |||
14-94309791-T-A | Inborn genetic diseases | Uncertain significance (Jan 09, 2024) | ||
14-94309801-C-T | Inborn genetic diseases | Uncertain significance (Jul 19, 2022) | ||
14-94309816-C-T | SERPINA6-related disorder | Benign (Sep 30, 2019) | ||
14-94309882-C-T | SERPINA6-related disorder | Benign (Nov 12, 2019) | ||
14-94309899-T-C | Inborn genetic diseases | Uncertain significance (Oct 12, 2022) | ||
14-94309910-G-A | Inborn genetic diseases | Uncertain significance (Nov 30, 2022) | ||
14-94309955-T-A | Inborn genetic diseases | Uncertain significance (Dec 14, 2021) | ||
14-94314042-A-G | Inborn genetic diseases | Uncertain significance (Dec 17, 2023) | ||
14-94314110-C-T | Corticosteroid-binding globulin deficiency | Uncertain significance (Jul 30, 2020) | ||
14-94314197-T-C | Inborn genetic diseases | Uncertain significance (Dec 19, 2023) | ||
14-94314271-G-A | SERPINA6-related disorder | Benign (Jan 19, 2021) | ||
14-94314305-A-T | Corticosteroid-binding globulin deficiency • SERPINA6-related disorder | Conflicting classifications of pathogenicity (Dec 07, 2023) | ||
14-94314456-T-C | Inborn genetic diseases | Uncertain significance (Dec 28, 2022) | ||
14-94314483-CCA-C | Corticosteroid-binding globulin deficiency | Likely pathogenic (May 11, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SERPINA6 | protein_coding | protein_coding | ENST00000341584 | 4 | 19147 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
8.34e-7 | 0.312 | 125720 | 0 | 26 | 125746 | 0.000103 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.662 | 244 | 217 | 1.13 | 0.0000124 | 2685 |
Missense in Polyphen | 59 | 58.942 | 1.001 | 830 | ||
Synonymous | -0.647 | 97 | 89.2 | 1.09 | 0.00000537 | 800 |
Loss of Function | 0.367 | 10 | 11.3 | 0.882 | 4.99e-7 | 142 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000702 | 0.000702 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000704 | 0.0000703 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.0000653 | 0.0000653 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Major transport protein for glucocorticoids and progestins in the blood of almost all vertebrate species. {ECO:0000269|PubMed:18513745}.;
- Disease
- DISEASE: Corticosteroid-binding globulin deficiency (CBG deficiency) [MIM:611489]: Extremely rare hereditary disorder characterized by reduced corticosteroid-binding capacity with normal or low plasma corticosteroid-binding globulin concentration, and normal or low basal cortisol levels associated with hypo/hypertension and muscle fatigue. {ECO:0000269|PubMed:10634411, ECO:0000269|PubMed:1504007, ECO:0000269|PubMed:17245537, ECO:0000269|PubMed:8212073}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Glucocorticoid Pathway (Peripheral Tissue), Pharmacodynamics
(Consensus)
Recessive Scores
- pRec
- 0.212
Intolerance Scores
- loftool
- 0.173
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.51
Haploinsufficiency Scores
- pHI
- 0.245
- hipred
- N
- hipred_score
- 0.123
- ghis
- 0.426
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.160
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Serpina6
- Phenotype
- homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype;
Gene ontology
- Biological process
- glucocorticoid metabolic process;negative regulation of endopeptidase activity
- Cellular component
- extracellular space;extracellular exosome
- Molecular function
- serine-type endopeptidase inhibitor activity;steroid binding