SEMA4G

semaphorin 4G, the group of Immunoglobulin like domain containing|Semaphorins|MicroRNA protein coding host genes

Basic information

Region (hg38): 10:100969504-100985871

Links

ENSG00000095539 ∙ NCBI:57715 ∙ OMIM:618991 ∙ HGNC:10735 ∙ Uniprot:Q9NTN9 ∙ 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 SEMA4G gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA4G 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	3	4
missense			61	1	2	64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	61	2	5

Variants in SEMA4G

This is a list of pathogenic ClinVar variants found in the SEMA4G region.

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

Position	Type	Phenotype	Significance	ClinVar
10-100972951-C-T			Likely benign (Jun 28, 2018)
10-100972962-C-A		not specified	Uncertain significance (Jun 07, 2023)
10-100973027-C-T		not specified	Uncertain significance (Feb 07, 2023)
10-100973155-G-A		not specified	Uncertain significance (Jul 20, 2021)
10-100973162-C-T		not specified	Uncertain significance (Jan 27, 2022)
10-100973209-C-A		not specified	Uncertain significance (Aug 10, 2023)
10-100973218-G-A		not specified	Uncertain significance (Jan 24, 2024)
10-100973222-G-A		not specified	Uncertain significance (Nov 27, 2023)
10-100973251-G-T		not specified	Uncertain significance (Dec 06, 2021)
10-100973270-A-G		not specified	Uncertain significance (May 05, 2023)
10-100973591-A-C		not specified	Uncertain significance (Aug 09, 2021)
10-100977647-C-T		not specified	Uncertain significance (Oct 26, 2022)
10-100977653-C-T		not specified	Uncertain significance (Dec 21, 2022)
10-100977666-G-A		not specified	Uncertain significance (Mar 07, 2023)
10-100977677-A-G		not specified	Uncertain significance (Nov 17, 2023)
10-100977701-C-G		not specified	Uncertain significance (Feb 16, 2023)
10-100977729-T-C		not specified	Uncertain significance (Dec 11, 2023)
10-100978305-C-A		not specified	Uncertain significance (May 05, 2023)
10-100978333-G-C		not specified	Uncertain significance (Aug 12, 2022)
10-100978364-C-T		not specified	Uncertain significance (Dec 06, 2022)
10-100978365-G-A		not specified	Uncertain significance (Sep 16, 2021)
10-100978532-G-A		not specified	Uncertain significance (Dec 19, 2022)
10-100978583-C-T		not specified	Uncertain significance (Jan 06, 2023)
10-100978625-A-G		not specified	Uncertain significance (Jan 04, 2022)
10-100978875-G-A		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA4G	protein_coding	protein_coding	ENST00000210633	14	16354

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-8	0.998	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.953	456	517	0.882	0.0000330	5338
Missense in Polyphen		182	221.68	0.821		2295
Synonymous	1.11	181	201	0.901	0.0000109	1850
Loss of Function	2.73	19	36.9	0.515	0.00000208	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000179	0.000179
Ashkenazi Jewish	0.00	0.00
East Asian	0.000545	0.000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000444	0.000440
Middle Eastern	0.000545	0.000544
South Asian	0.000165	0.000163
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface receptor for PLXNB2. May play a role in axon guidance (By similarity). {ECO:0000250}.
• Pathway: Axon guidance - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.758
• rvis_EVS: -1.13
• rvis_percentile_EVS: 6.56

Haploinsufficiency Scores

• pHI: 0.164
• hipred: Y
• hipred_score: 0.605
• ghis: 0.644

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.859

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sema4g
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; renal/urinary system phenotype; normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: neural crest cell migration;positive regulation of cell migration;negative regulation of axon extension involved in axon guidance;negative chemotaxis;semaphorin-plexin signaling pathway
• Cellular component: extracellular space;integral component of plasma membrane
• Molecular function: protein binding;semaphorin receptor binding;neuropilin binding;chemorepellent activity