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GeneBe

SEMA3D

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

Basic information

Region (hg38): 7:84995552-85187056

Links

ENSG00000153993NCBI:223117OMIM:609907HGNC:10726Uniprot:O95025AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA3D gene.

  • not provided (32 variants)
  • Inborn genetic diseases (28 variants)
  • SEMA3D-related condition (18 variants)
  • Progressive sensorineural hearing impairment (1 variants)
  • Aganglionic megacolon (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.

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
41
clinvar
1
clinvar
1
clinvar
44
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
2
4
non coding
1
clinvar
4
clinvar
5
Total 1 0 41 13 12

Highest pathogenic variant AF is 0.00000659

Variants in SEMA3D

This is a list of pathogenic ClinVar variants found in the SEMA3D region.

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

Position Type Phenotype Significance ClinVar
7-84999443-C-T SEMA3D-related condition Likely benign (Jun 17, 2021)734359
7-84999451-C-T not specified Uncertain significance (Aug 30, 2022)2389063
7-84999457-T-C SEMA3D-related condition Uncertain significance (Jan 09, 2024)2629052
7-84999563-C-T SEMA3D-related condition Likely benign (Oct 18, 2022)2657653
7-84999580-C-T SEMA3D-related condition Uncertain significance (Jan 25, 2024)2636865
7-84999581-G-A SEMA3D-related condition Likely benign (Nov 04, 2022)3030163
7-84999598-T-C SEMA3D-related condition Uncertain significance (Aug 31, 2023)2634320
7-84999623-G-T SEMA3D-related condition Likely benign (Nov 08, 2021)3029219
7-84999627-T-C SEMA3D-related condition Uncertain significance (Oct 25, 2023)3032263
7-84999645-C-T not specified Uncertain significance (Dec 18, 2023)3159717
7-84999673-T-G SEMA3D-related condition Benign (Jul 19, 2022)3060976
7-84999713-T-C SEMA3D-related condition Likely benign (Jan 07, 2020)3051634
7-84999734-A-T SEMA3D-related condition Likely benign (Jun 21, 2022)3049025
7-84999747-A-G SEMA3D-related condition Conflicting classifications of pathogenicity (Nov 21, 2023)2636517
7-84999799-C-A not specified Uncertain significance (May 27, 2022)2292272
7-84999809-C-A not specified Uncertain significance (Feb 15, 2023)2484437
7-84999817-G-C SEMA3D-related condition Uncertain significance (Oct 11, 2023)2634977
7-84999836-C-T SEMA3D-related condition Likely benign (May 26, 2021)742221
7-84999837-G-A not specified Uncertain significance (Sep 27, 2021)3159714
7-84999854-A-C not specified Uncertain significance (Jan 10, 2023)2475328
7-85006809-C-T SEMA3D-related condition Uncertain significance (Dec 28, 2023)3055058
7-85006842-T-G SEMA3D-related condition • not specified Uncertain significance (Jan 09, 2024)2512535
7-85006862-T-A not specified Uncertain significance (Sep 14, 2022)2311824
7-85006867-G-T SEMA3D-related condition Likely benign (Jan 01, 2024)782021
7-85012788-C-T not specified Uncertain significance (Jul 06, 2021)2234970

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA3Dprotein_codingprotein_codingENST00000284136 17191303
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.02e-81.001257070411257480.000163
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7553714140.8960.00002115127
Missense in Polyphen141173.640.812022135
Synonymous-0.3031511461.030.000007521416
Loss of Function3.372044.20.4520.00000248529

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001210.000121
Ashkenazi Jewish0.000.00
East Asian0.0001800.000163
Finnish0.00009280.0000924
European (Non-Finnish)0.0002310.000229
Middle Eastern0.0001800.000163
South Asian0.0001970.000196
Other0.0001720.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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