SEMA3G

semaphorin 3G, the group of Immunoglobulin like domain containing|Semaphorins

Basic information

Region (hg38): 3:52433035-52445103

Links

ENSG00000010319 ∙ NCBI:56920 ∙ ∙ HGNC:30400 ∙ Uniprot:Q9NS98 ∙ 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 SEMA3G gene.

• SEMA3G-related_disorder (281 variants)
• not_specified (140 variants)
• not_provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA3G gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020163.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	90	2	94
missense			218	16		234
nonsense			6	1		7
start loss						0
frameshift			7			7
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	234	107	2

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA3G	protein_coding	protein_coding	ENST00000231721	16	12033

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.26e-18	0.172	125556	1	191	125748	0.000764

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.380	475	499	0.952	0.0000345	4986
Missense in Polyphen		202	214.18	0.94313		2131
Synonymous	0.690	194	207	0.939	0.0000134	1682
Loss of Function	1.36	32	41.4	0.772	0.00000244	398

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00440	0.00440
Ashkenazi Jewish	0.000700	0.000695
East Asian	0.000164	0.000163
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000534	0.000528
Middle Eastern	0.000164	0.000163
South Asian	0.00103	0.000980
Other	0.000816	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has chemorepulsive activities for sympathetic axons. Ligand of NRP2 (By similarity). {ECO:0000250}.
• Pathway: Axon guidance - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.897
• rvis_EVS: -0.66
• rvis_percentile_EVS: 16.07

Haploinsufficiency Scores

• pHI: 0.145
• hipred: N
• hipred_score: 0.229
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.591

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sema3g
• Phenotype: immune system phenotype; normal phenotype

Gene ontology

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