SEMA3G

protein-coding

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

Gene summary

The transcription of this gene is activated by PPAR-gamma, and the resulting protein product plays a role in endothelial cell migration. Expression of this gene also inhibits tumor cell migration and invasion. [provided by RefSeq, Jul 2016]

MANE transcript

NM_020163.3

Inheritance

—

ClinVar variants

U:345B:134

Top phenotype

SEMA3G-related disorder

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr3:52,433,035-52,445,103

External References & Databases

Ensembl (ENSG00000010319)

Transcript & Mutation Effects

hg38 • Region Span ~12.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SEMA3G variants in ClinVar

3 Conditions Cataloged

SEMA3G-related disorderTotal: 440

not specifiedTotal: 152

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020163.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	115 clinvar	2 clinvar	121
missense			312 clinvar	16 clinvar		328
nonsense			7 clinvar	1 clinvar		8
start loss						0
frameshift			13 clinvar			13
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	345	132	2	479

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020163.3	RefSeq	NP_064548.1	16	MANE Select
ENST00000231721.7	Ensembl	ENSP00000231721.2	16	MANE Select
ENST00000465657.1	Ensembl	ENSP00000420291.1	4	Standard
ENST00000475739.1	Ensembl	ENSP00000419181.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Axon guidance - Homo sapiens (human)

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

Molecular Function

signaling receptor binding
semaphorin receptor binding
neuropilin binding
chemorepellent activity

Cellular Component

extracellular space
integral component of plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000231721
Coding exons: 16
Length: 12033
Individuals with no LoFs: 125556
Homozygous LoFs: 1
Heterozygous LoFs: 191
Defined: 125748
p: 0.000764

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.380	475	499	0.952	0.0000345	4986
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0038	0.0038	notable
Latino/Admixed American	0.00064	0.00064	rare
Ashkenazi Jewish	0.00070	0.00069	rare
East Asian	0.00016	0.00016	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00053	0.00053	rare
South Asian	0.0010	0.00098	notable
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Has chemorepulsive activities for sympathetic axons. Ligand of NRP2 (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.897
RVIS EVS: -0.66
RVIS percentile EVS: 16.07

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.591

Gene Damage Prediction

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