SEMA3D

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

Basic information

Region (hg38): 7:84995552-85187056

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.

• 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	7	18
missense	1		41	1	1	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding				1	4	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 disorder	Likely benign (Jun 17, 2021)
7-84999451-C-T		not specified	Uncertain significance (Aug 30, 2022)
7-84999457-T-C		SEMA3D-related disorder	Uncertain significance (Jan 09, 2024)
7-84999563-C-T		SEMA3D-related disorder	Likely benign (Oct 18, 2022)
7-84999580-C-T		SEMA3D-related disorder	Uncertain significance (Jan 25, 2024)
7-84999581-G-A		SEMA3D-related disorder	Likely benign (Nov 04, 2022)
7-84999598-T-C		SEMA3D-related disorder	Uncertain significance (Aug 31, 2023)
7-84999623-G-T		SEMA3D-related disorder	Likely benign (Nov 08, 2021)
7-84999627-T-C		SEMA3D-related disorder	Uncertain significance (Oct 25, 2023)
7-84999645-C-T		not specified	Uncertain significance (Dec 18, 2023)
7-84999673-T-G		SEMA3D-related disorder	Benign (Jul 19, 2022)
7-84999713-T-C		SEMA3D-related disorder	Likely benign (Jan 07, 2020)
7-84999734-A-T		SEMA3D-related disorder	Likely benign (Jun 21, 2022)
7-84999747-A-G		SEMA3D-related disorder	Conflicting classifications of pathogenicity (Nov 21, 2023)
7-84999799-C-A		not specified	Uncertain significance (May 27, 2022)
7-84999809-C-A		not specified	Uncertain significance (Feb 15, 2023)
7-84999817-G-C		SEMA3D-related disorder	Uncertain significance (Oct 11, 2023)
7-84999836-C-T		SEMA3D-related disorder	Likely benign (May 26, 2021)
7-84999837-G-A		not specified	Uncertain significance (Sep 27, 2021)
7-84999854-A-C		not specified	Uncertain significance (Jan 10, 2023)
7-85006809-C-T		SEMA3D-related disorder	Uncertain significance (Dec 28, 2023)
7-85006842-T-G		SEMA3D-related disorder • not specified	Uncertain significance (Jan 09, 2024)
7-85006862-T-A		not specified	Uncertain significance (Sep 14, 2022)
7-85006867-G-T		SEMA3D-related disorder	Likely benign (Jan 01, 2024)
7-85012788-C-T		not specified	Uncertain significance (Jul 06, 2021)

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