SCML2
Basic information
Region (hg38): X:18239312-18354688
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCML2 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 | 13 | 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 | 13 | 3 | 0 |
Variants in SCML2
This is a list of pathogenic ClinVar variants found in the SCML2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
X-18246675-C-T | not specified | Likely benign (May 24, 2023) | ||
X-18256860-T-C | not specified | Uncertain significance (Jan 18, 2022) | ||
X-18256934-T-C | not specified | Uncertain significance (Oct 05, 2021) | ||
X-18257008-A-C | not specified | Uncertain significance (Feb 16, 2023) | ||
X-18258051-C-T | Likely benign (Sep 01, 2022) | |||
X-18258073-G-C | not specified | Uncertain significance (Dec 17, 2023) | ||
X-18258100-G-C | not specified | Likely benign (Apr 24, 2024) | ||
X-18258157-G-C | not specified | Uncertain significance (Feb 17, 2024) | ||
X-18258170-A-G | not specified | Uncertain significance (May 14, 2024) | ||
X-18260224-C-T | not specified | Uncertain significance (Oct 06, 2022) | ||
X-18260228-G-A | not specified | Uncertain significance (Aug 02, 2023) | ||
X-18260273-T-C | not specified | Uncertain significance (Mar 20, 2024) | ||
X-18265676-A-C | not specified | Uncertain significance (Mar 28, 2024) | ||
X-18265730-G-A | not specified | Uncertain significance (Sep 06, 2022) | ||
X-18265733-G-A | not specified | Uncertain significance (Jun 01, 2023) | ||
X-18265758-C-T | not specified | Likely benign (Aug 13, 2021) | ||
X-18305088-G-A | not specified | Uncertain significance (Jul 19, 2023) | ||
X-18305106-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
X-18324029-T-C | not specified | Uncertain significance (Apr 23, 2024) | ||
X-18330619-G-A | not specified | Uncertain significance (Dec 28, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SCML2 | protein_coding | protein_coding | ENST00000251900 | 14 | 115414 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 0.000387 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.40 | 149 | 257 | 0.579 | 0.0000190 | 4588 |
Missense in Polyphen | 29 | 92.053 | 0.31503 | 1594 | ||
Synonymous | 1.69 | 73 | 93.8 | 0.778 | 0.00000698 | 1362 |
Loss of Function | 4.40 | 0 | 22.6 | 0.00 | 0.00000168 | 410 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Putative Polycomb group (PcG) protein. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0950
Intolerance Scores
- loftool
- 0.135
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.09
Haploinsufficiency Scores
- pHI
- 0.128
- hipred
- Y
- hipred_score
- 0.627
- ghis
- 0.578
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.487
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Scml2
- Phenotype
- reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;anatomical structure morphogenesis
- Cellular component
- nucleus;PcG protein complex
- Molecular function
- DNA binding;DNA-binding transcription factor activity;protein binding