Menu
GeneBe

SEMG1

semenogelin 1

Basic information

Region (hg38): 20:45207032-45209768

Previous symbols: [ "SEMG" ]

Links

ENSG00000124233NCBI:6406OMIM:182140HGNC:10742Uniprot:P04279AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMG1 gene.

  • Inborn genetic diseases (28 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMG1 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
3
clinvar
28
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 3 0

Variants in SEMG1

This is a list of pathogenic ClinVar variants found in the SEMG1 region.

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

Position Type Phenotype Significance ClinVar
20-45207118-T-C not specified Uncertain significance (Feb 14, 2023)2456998
20-45207395-C-T not specified Uncertain significance (Dec 01, 2022)2331441
20-45207485-T-C not specified Uncertain significance (Feb 06, 2024)3159938
20-45207487-T-C not specified Uncertain significance (Dec 17, 2021)2379698
20-45207491-T-C not specified Uncertain significance (Aug 08, 2023)2617515
20-45207515-C-T not specified Uncertain significance (Jul 26, 2022)2208968
20-45207541-A-C not specified Uncertain significance (Jun 03, 2022)2293976
20-45207562-G-A not specified Uncertain significance (Mar 23, 2023)2528823
20-45207632-A-G not specified Uncertain significance (Jun 29, 2023)2608062
20-45207635-G-A not specified Uncertain significance (Sep 14, 2022)2394909
20-45207644-A-G not specified Uncertain significance (Dec 31, 2023)3159939
20-45207692-G-A not specified Uncertain significance (Jul 19, 2022)2302046
20-45207697-A-C not specified Likely benign (Dec 02, 2022)2373147
20-45207740-A-C not specified Uncertain significance (Feb 06, 2024)3159940
20-45207811-A-C not specified Uncertain significance (May 11, 2022)2288779
20-45207862-G-A not specified Uncertain significance (Apr 08, 2022)2406581
20-45207931-A-G not specified Uncertain significance (Aug 23, 2021)2362542
20-45207935-C-T not specified Uncertain significance (Feb 07, 2023)2458561
20-45207944-A-G not specified Uncertain significance (Feb 05, 2024)3159941
20-45207986-A-T not specified Uncertain significance (May 18, 2023)2564901
20-45207993-T-A not specified Uncertain significance (May 26, 2023)2512418
20-45208052-A-G not specified Uncertain significance (Dec 07, 2023)3159943
20-45208101-C-G not specified Uncertain significance (Dec 14, 2023)3159944
20-45208129-C-G not specified Likely benign (Aug 04, 2021)2409919
20-45208155-A-G not specified Uncertain significance (May 04, 2022)2287337

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMG1protein_codingprotein_codingENST00000372781 22776
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.3570.595125675021256770.00000796
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.5702652401.100.00001183055
Missense in Polyphen109103.671.05141449
Synonymous-1.7910886.81.240.00000417839
Loss of Function1.5514.590.2182.81e-744

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005460.0000544
Finnish0.000.00
European (Non-Finnish)0.000008800.00000880
Middle Eastern0.00005460.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Predominant protein in semen. It participates in the formation of a gel matrix entrapping the accessory gland secretions and ejaculated spermatozoa. Fragments of semenogelin and/or fragments of the related proteins may contribute to the activation of progressive sperm movements as the gel-forming proteins are fragmented by KLK3/PSA. {ECO:0000269|PubMed:19889947}.;
Pathway
Antimicrobial peptides;Innate Immune System;Immune System (Consensus)

Recessive Scores

pRec
0.110

Intolerance Scores

loftool
0.946
rvis_EVS
0.89
rvis_percentile_EVS
89.24

Haploinsufficiency Scores

pHI
0.0379
hipred
N
hipred_score
0.133
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.279

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
insemination;antimicrobial humoral response;antibacterial humoral response;killing of cells of other organism;cellular protein metabolic process;sperm capacitation;coagulation;protein heterooligomerization;antimicrobial humoral immune response mediated by antimicrobial peptide;negative regulation of calcium ion import;positive regulation of serine-type endopeptidase activity;negative regulation of flagellated sperm motility
Cellular component
extracellular region;extracellular space;nucleus;protein-containing complex;extracellular exosome
Molecular function
protein binding;zinc ion binding