SEMG2

semenogelin 2

Basic information

Region (hg38): 20:45221373-45224458

Links

ENSG00000124157 ∙ NCBI:6407 ∙ OMIM:182141 ∙ HGNC:10743 ∙ Uniprot:Q02383 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	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)
20-45221423-C-T		not specified	Uncertain significance (Jan 03, 2024)
20-45221430-T-C		not specified	Uncertain significance (Sep 04, 2024)
20-45221448-C-G		not specified	Uncertain significance (Jan 25, 2023)
20-45221738-T-A		not specified	Uncertain significance (Sep 16, 2021)
20-45221750-C-A		not specified	Uncertain significance (Sep 29, 2023)
20-45221778-T-C		not specified	Likely benign (Mar 07, 2023)
20-45221838-A-T		not specified	Uncertain significance (Jul 26, 2022)
20-45221871-G-A		not specified	Uncertain significance (Oct 16, 2024)
20-45221905-T-A		not specified	Uncertain significance (Dec 02, 2024)
20-45222029-G-A		not specified	Uncertain significance (Feb 10, 2022)
20-45222030-G-A		not specified	Uncertain significance (Oct 12, 2024)
20-45222042-A-G		not specified	Likely benign (Apr 18, 2024)
20-45222072-G-A		not specified	Uncertain significance (Dec 19, 2022)
20-45222131-T-C		not specified	Uncertain significance (Apr 13, 2022)
20-45222135-T-C		not specified	Uncertain significance (Oct 25, 2024)
20-45222141-G-A		not specified	Uncertain significance (Feb 06, 2023)
20-45222143-C-A		not specified	Uncertain significance (Oct 17, 2023)
20-45222150-A-C		not specified	Uncertain significance (Feb 06, 2023)
20-45222254-C-T		not specified	Uncertain significance (Mar 30, 2022)
20-45222255-G-A		not specified	Uncertain significance (Jul 20, 2021)
20-45222266-A-C		not specified	Uncertain significance (Sep 18, 2024)
20-45222333-T-G		not specified	Uncertain significance (Jul 05, 2022)
20-45222350-C-T		not specified	Uncertain significance (Aug 12, 2021)
20-45222395-A-T		not specified	Uncertain significance (Sep 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMG2	protein_coding	protein_coding	ENST00000372769	2	3159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0582	0.728	125720	0	18	125738	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.26	358	297	1.21	0.0000140	3883
Missense in Polyphen		135	122.45	1.1025		1716
Synonymous	-1.42	125	106	1.18	0.00000515	1039
Loss of Function	0.787	2	3.61	0.553	1.53e-7	41

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.000470	0.000457
Other	0.00	0.00

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

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.227

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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