SERAC1
Basic information
Region (hg38): 6:158109519-158168280
Links
Phenotypes
GenCC
Source:
- 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome (Strong), mode of inheritance: AR
- 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome (Supportive), mode of inheritance: AR
- 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome (Definitive), mode of inheritance: AR
- 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome (Strong), mode of inheritance: AR
- Leigh syndrome (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | 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 | Audiologic/Otolaryngologic; Biochemical; Neurologic | 16527507; 22683713; 23707711 |
ClinVar
This is a list of variants' phenotypes submitted to
- 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome (23 variants)
- not provided (9 variants)
- Inborn genetic diseases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERAC1 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 | 48 | 55 | ||||
missense | 95 | 113 | ||||
nonsense | 11 | 15 | ||||
start loss | 0 | |||||
frameshift | 10 | 16 | ||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 3 | 11 | 12 | 26 | ||
non coding | 97 | 44 | 153 | |||
Total | 26 | 17 | 110 | 153 | 50 |
Highest pathogenic variant AF is 0.000151
Variants in SERAC1
This is a list of pathogenic ClinVar variants found in the SERAC1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
6-158111064-ACT-A | Likely benign (Jul 09, 2018) | |||
6-158111108-C-T | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Benign (May 02, 2023) | ||
6-158111155-A-G | Benign (Jun 14, 2018) | |||
6-158111350-T-C | not specified | Benign (Jun 16, 2014) | ||
6-158111364-TGTTA-T | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (Nov 24, 2022) | ||
6-158111366-T-C | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (Aug 19, 2022) | ||
6-158111369-G-C | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (Aug 17, 2021) | ||
6-158111397-C-T | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (Nov 22, 2022) | ||
6-158111398-G-A | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome • SERAC1-related disorder | Benign/Likely benign (Dec 09, 2023) | ||
6-158111400-ATGAAT-A | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (Jul 13, 2022) | ||
6-158111415-C-G | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Conflicting classifications of pathogenicity (Nov 01, 2022) | ||
6-158111415-C-T | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (Aug 10, 2022) | ||
6-158111416-G-A | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (Nov 22, 2022) | ||
6-158111455-T-C | Inborn genetic diseases | Uncertain significance (Dec 19, 2022) | ||
6-158111480-A-AT | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Pathogenic (-) | ||
6-158111483-T-C | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Likely benign (Feb 03, 2023) | ||
6-158111485-G-T | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (May 10, 2023) | ||
6-158111488-C-T | Uncertain significance (-) | |||
6-158111492-A-T | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (Jun 09, 2022) | ||
6-158111508-G-C | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (Nov 29, 2022) | ||
6-158113420-C-T | Likely benign (Oct 01, 2022) | |||
6-158113439-G-C | not specified • 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Likely benign (Oct 23, 2023) | ||
6-158113439-GAGTGAATACCTGCTGA-CCTGTTGGT | SERAC1-related disorder • 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Pathogenic/Likely pathogenic (Jun 24, 2024) | ||
6-158113446-T-C | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (Feb 08, 2018) | ||
6-158113452-C-T | 3-methylglutaconic aciduria with deafness, encephalopathy, and Leigh-like syndrome | Uncertain significance (Apr 16, 2021) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SERAC1 | protein_coding | protein_coding | ENST00000367104 | 16 | 58777 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00000393 | 1.00 | 125637 | 0 | 111 | 125748 | 0.000441 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.49 | 278 | 357 | 0.778 | 0.0000187 | 4271 |
Missense in Polyphen | 66 | 114.02 | 0.57885 | 1308 | ||
Synonymous | 1.49 | 100 | 121 | 0.828 | 0.00000630 | 1240 |
Loss of Function | 3.39 | 16 | 38.8 | 0.412 | 0.00000225 | 447 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000907 | 0.000898 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000381 | 0.000381 |
Finnish | 0.00171 | 0.00171 |
European (Non-Finnish) | 0.000256 | 0.000255 |
Middle Eastern | 0.000381 | 0.000381 |
South Asian | 0.000425 | 0.000425 |
Other | 0.000327 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Plays an important role in the phosphatidylglycerol remodeling that is essential for both mitochondrial function and intracellular cholesterol trafficking. May catalyze the remodeling of phosphatidylglycerol and be involved in the transacylation- acylation reaction to produce phosphatidylglycerol-36:1. May be involved in bis(monoacylglycerol)phosphate biosynthetic pathway. {ECO:0000269|PubMed:22683713}.;
Recessive Scores
- pRec
- 0.0972
Intolerance Scores
- loftool
- 0.440
- rvis_EVS
- 0.24
- rvis_percentile_EVS
- 69.51
Haploinsufficiency Scores
- pHI
- 0.198
- hipred
- N
- hipred_score
- 0.492
- ghis
- 0.468
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.168
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Serac1
- Phenotype
Gene ontology
- Biological process
- phospholipid biosynthetic process;extracellular matrix organization;intracellular cholesterol transport;phosphatidylglycerol acyl-chain remodeling
- Cellular component
- mitochondrion;endoplasmic reticulum;integral component of membrane;extracellular matrix;mitochondria-associated endoplasmic reticulum membrane
- Molecular function
- molecular_function