SEMA3D

semaphorin 3D, the group of Semaphorins|V-set domain containing

Basic information

Region (hg38): 7:84995553-85187056

Links

ENSG00000153993

∙ NCBI:223117 ∙ OMIM:609907 ∙ HGNC:10726 ∙ Uniprot:O95025 ∙ 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 SEMA3D gene.

Progressive sensorineural hearing impairment (1 variants)
SEMA3D-related disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA3D gene is commonly pathogenic or not. These statistics are base on trasncript: . 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				11 clinvar	7 clinvar	18
missense	1 clinvar		59 clinvar	4 clinvar	1 clinvar	65
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	59	15	8

Highest pathogenic variant AF is 0.00000658987

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SEMA3D	protein_coding	protein_coding	ENST00000284136	17	191303

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.02e-8	1.00	125707	0	41	125748	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.755	371	414	0.896	0.0000211	5127
Missense in Polyphen		141	173.64	0.81202		2135
Synonymous	-0.303	151	146	1.03	0.00000752	1416
Loss of Function	3.37	20	44.2	0.452	0.00000248	529

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000121	0.000121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000180	0.000163
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000231	0.000229
Middle Eastern	0.000180	0.000163
South Asian	0.000197	0.000196
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Induces the collapse and paralysis of neuronal growth cones. Could potentially act as repulsive cues toward specific neuronal populations. Binds to neuropilin (By similarity). {ECO:0000250}.;
Pathway: Axon guidance - Homo sapiens (human) (Consensus)

Intolerance Scores

loftool: 0.718
rvis_EVS: -0.26
rvis_percentile_EVS: 34.88

Haploinsufficiency Scores

pHI: 0.638
hipred: Y
hipred_score: 0.544
ghis: 0.509

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.120

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Sema3d
Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);

Zebrafish Information Network

Gene name: sema3d
Affected structure: Rohon-Beard neuron
Phenotype tag: abnormal
Phenotype quality: decreased amount

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: semaphorin receptor binding;neuropilin binding;chemorepellent activity