SMCP
Basic information
Region (hg38): 1:152878322-152885047
Previous symbols: [ "MCSP" ]
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 SMCP 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 | 0 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in SMCP
This is a list of pathogenic ClinVar variants found in the SMCP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-152884488-G-T | not specified | Uncertain significance (Feb 09, 2025) | ||
| 1-152884499-G-C | not specified | Uncertain significance (Jan 21, 2025) | ||
| 1-152884502-G-A | not specified | Uncertain significance (Feb 07, 2025) | ||
| 1-152884540-A-C | not specified | Uncertain significance (Mar 07, 2025) | ||
| 1-152884579-C-T | not specified | Uncertain significance (Oct 04, 2022) | ||
| 1-152884632-G-T | not specified | Uncertain significance (Aug 10, 2021) | ||
| 1-152884697-C-T | not specified | Uncertain significance (Sep 11, 2024) | ||
| 1-152884709-A-G | not specified | Uncertain significance (Jul 27, 2024) | ||
| 1-152884744-C-T | not specified | Uncertain significance (Dec 11, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SMCP | protein_coding | protein_coding | ENST00000368765 | 1 | 6731 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.136 | 61 | 58.1 | 1.05 | 0.00000263 | 779 |
| Missense in Polyphen | 4 | 2.5574 | 1.5641 | 27 | ||
| Synonymous | -0.112 | 22 | 21.3 | 1.03 | 0.00000103 | 189 |
| Loss of Function |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | ||
| East Asian | ||
| Finnish | ||
| European (Non-Finnish) | ||
| Middle Eastern | ||
| South Asian | ||
| Other |
dbNSFP
Source:
- Function
- FUNCTION: Involved in sperm motility. Its absence is associated with genetic background dependent male infertility. Infertility may be due to reduced sperm motility in the female reproductive tract and inability to penetrate the oocyte zona pellucida (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.207
Intolerance Scores
- loftool
- 0.669
- rvis_EVS
- 0.44
- rvis_percentile_EVS
- 77.45
Haploinsufficiency Scores
- pHI
- 0.0673
- hipred
- N
- hipred_score
- 0.123
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.973
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Smcp
- Phenotype
- cellular phenotype; reproductive system phenotype;
Gene ontology
- Biological process
- penetration of zona pellucida;flagellated sperm motility
- Cellular component
- cytoplasm;mitochondrion;mitochondrial membrane
- Molecular function
- molecular_function;protein binding