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GeneBe

SEMG2

semenogelin 2

Basic information

Region (hg38): 20:45221372-45224458

Links

ENSG00000124157NCBI:6407OMIM:182141HGNC:10743Uniprot:Q02383AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMG2 gene.

  • Inborn genetic diseases (27 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMG2 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
25
clinvar
2
clinvar
27
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 25 2 0

Variants in SEMG2

This is a list of pathogenic ClinVar variants found in the SEMG2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
20-45221418-C-A not specified Uncertain significance (Jan 23, 2023)2464661
20-45221423-C-T not specified Uncertain significance (Jan 03, 2024)3159949
20-45221448-C-G not specified Uncertain significance (Jan 25, 2023)2458874
20-45221738-T-A not specified Uncertain significance (Sep 16, 2021)2250424
20-45221750-C-A not specified Uncertain significance (Sep 29, 2023)3159946
20-45221778-T-C not specified Likely benign (Mar 07, 2023)2457402
20-45221838-A-T not specified Uncertain significance (Jul 26, 2022)2210140
20-45222029-G-A not specified Uncertain significance (Feb 10, 2022)2230301
20-45222072-G-A not specified Uncertain significance (Dec 19, 2022)3159950
20-45222131-T-C not specified Uncertain significance (Apr 13, 2022)2385459
20-45222141-G-A not specified Uncertain significance (Feb 06, 2023)2468991
20-45222143-C-A not specified Uncertain significance (Oct 17, 2023)3159951
20-45222150-A-C not specified Uncertain significance (Feb 06, 2023)2468992
20-45222254-C-T not specified Uncertain significance (Mar 30, 2022)2411440
20-45222255-G-A not specified Uncertain significance (Jul 20, 2021)2377931
20-45222333-T-G not specified Uncertain significance (Jul 05, 2022)2292273
20-45222350-C-T not specified Uncertain significance (Aug 12, 2021)2371255
20-45222440-A-G not specified Uncertain significance (Jan 23, 2023)2477145
20-45222506-C-G not specified Uncertain significance (Aug 02, 2023)2615649
20-45222507-G-A not specified Uncertain significance (Apr 06, 2023)2552995
20-45222638-G-T not specified Uncertain significance (Sep 20, 2023)3159945
20-45222776-A-G not specified Uncertain significance (Sep 01, 2021)2247847
20-45222864-C-G not specified Uncertain significance (Nov 29, 2021)2262372
20-45222864-C-T not specified Uncertain significance (Dec 16, 2023)3159947
20-45222923-A-G not specified Uncertain significance (Apr 05, 2023)2532951

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMG2protein_codingprotein_codingENST00000372769 23159
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.05820.7281257200181257380.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.263582971.210.00001403883
Missense in Polyphen135122.451.10251716
Synonymous-1.421251061.180.000005151039
Loss of Function0.78723.610.5531.53e-741

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001210.000121
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.00005440.0000544
South Asian0.0004700.000457
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Participates in the formation of a gel matrix (sperm coagulum) entrapping the accessory gland secretions and ejaculated spermatozoa.;

Recessive Scores

pRec
0.0565

Intolerance Scores

loftool
0.981
rvis_EVS
1.07
rvis_percentile_EVS
91.68

Haploinsufficiency Scores

pHI
0.158
hipred
N
hipred_score
0.133
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.227

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
antibacterial humoral response;sperm capacitation;coagulation;protein heterooligomerization;positive regulation of serine-type endopeptidase activity;negative regulation of flagellated sperm motility
Cellular component
extracellular space;nucleus;extracellular exosome
Molecular function
protease binding;protein binding;zinc ion binding