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.

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.

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					2	2
missense			95	5		100
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	95	5	2

Variants in SEMA3G

This is a list of pathogenic ClinVar variants found in the SEMA3G region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52435599-C-G		SEMA3G-related disorder	Likely benign (Jun 30, 2023)
3-52435601-T-C		SEMA3G-related disorder	Likely benign (Jan 30, 2023)
3-52435606-C-T		SEMA3G-related disorder	Likely benign (Mar 18, 2022)
3-52435612-C-G		SEMA3G-related disorder	Uncertain significance (Sep 23, 2024)
3-52435612-C-T		SEMA3G-related disorder	Benign (Apr 11, 2022)
3-52435623-G-A		SEMA3G-related disorder	Uncertain significance (Jun 28, 2024)
3-52435626-G-A		SEMA3G-related disorder	Uncertain significance (Jan 18, 2024)
3-52435627-C-T		SEMA3G-related disorder	Likely benign (Jul 06, 2022)
3-52435631-C-T		not specified	Uncertain significance (Jul 14, 2024)
3-52435646-T-C		not specified	Uncertain significance (Feb 13, 2024)
3-52435647-G-C		SEMA3G-related disorder	Uncertain significance (May 17, 2024)
3-52435652-C-T		SEMA3G-related disorder	Uncertain significance (May 28, 2024)
3-52435653-G-A		not specified	Uncertain significance (Apr 17, 2024)
3-52435663-C-T		SEMA3G-related disorder	Likely benign (Feb 16, 2024)
3-52435666-C-T		SEMA3G-related disorder	Likely benign (Apr 14, 2022)
3-52435690-G-C		not specified	Uncertain significance (Mar 17, 2023)
3-52435692-TCTTGCCCCTGGCCTG-T		SEMA3G-related disorder	Uncertain significance (Jul 24, 2024)
3-52435699-C-T		SEMA3G-related disorder	Likely benign (Jun 18, 2021)
3-52435715-C-T		SEMA3G-related disorder	Uncertain significance (Jul 01, 2024)
3-52435716-G-A		SEMA3G-related disorder	Uncertain significance (Feb 22, 2024)
3-52435718-C-T		not specified	Uncertain significance (Mar 01, 2025)
3-52435721-C-T		SEMA3G-related disorder	Uncertain significance (Feb 08, 2024)
3-52435727-C-T		not specified	Uncertain significance (Dec 31, 2023)
3-52435728-G-A		not specified	Uncertain significance (May 31, 2023)
3-52435747-C-T		SEMA3G-related disorder	Likely benign (Aug 18, 2021)

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