Seroatlas · Human Serome Atlas

SEMA3D

Semaphorin-3D

Also known as: coll-2, SEM3D_HUMAN, Sema-Z2

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: O95025
Gene: SEMA3D
Ensembl: ENSG00000153993
Chromosome: 7
Canonical length: 777 aa
Protein class: Predicted intracellular proteins, Predicted secreted proteins
Subcellular location: Vesicles
Secretome location: Secreted in other tissues

OverviewNCBI Gene

This gene encodes a member of the semaphorin III family of secreted signaling proteins that are involved in axon guidance during neuronal development. The encoded protein contains an N-terminal Sema domain, an immunoglobulin like domain and a C-terminal basic domain. The protein encoded by this gene binds neuropilin and plays an important role in cardiovascular development. [provided by RefSeq, Aug 2016]

Canonical amino-acid sequenceUniProt

777 residues, UniProt reviewed canonical sequence.

>O95025|SEMA3D
     1  MNANKDERLK ARSQDFHLFP ALMMLSMTML FLPVTGTLKQ NIPRLKLTYK DLLLSNSCIP
    61  FLGSSEGLDF QTLLLDEERG RLLLGAKDHI FLLSLVDLNK NFKKIYWPAA KERVELCKLA
   121  GKDANTECAN FIRVLQPYNK THIYVCGTGA FHPICGYIDL GVYKEDIIFK LDTHNLESGR
   181  LKCPFDPQQP FASVMTDEYL YSGTASDFLG KDTAFTRSLG PTHDHHYIRT DISEHYWLNG
   241  AKFIGTFFIP DTYNPDDDKI YFFFRESSQE GSTSDKTILS RVGRVCKNDV GGQRSLINKW
   301  TTFLKARLIC SIPGSDGADT YFDELQDIYL LPTRDERNPV VYGVFTTTSS IFKGSAVCVY
   361  SMADIRAVFN GPYAHKESAD HRWVQYDGRI PYPRPGTCPS KTYDPLIKST RDFPDDVISF
   421  IKRHSVMYKS VYPVAGGPTF KRINVDYRLT QIVVDHVIAE DGQYDVMFLG TDIGTVLKVV
   481  SISKEKWNME EVVLEELQIF KHSSIILNME LSLKQQQLYI GSRDGLVQLS LHRCDTYGKA
   541  CADCCLARDP YCAWDGNACS RYAPTSKRRA RRQDVKYGDP ITQCWDIEDS ISHETADEKV
   601  IFGIEFNSTF LECIPKSQQA TIKWYIQRSG DEHREELKPD ERIIKTEYGL LIRSLQKKDS
   661  GMYYCKAQEH TFIHTIVKLT LNVIENEQME NTQRAEHEEG KVKDLLAESR LRYKDYIQIL
   721  SSPNFSLDQY CEQMWHREKR RQRNKGGPKW KHMQEMKKKR NRRHHRDLDE LPRAVAT

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SEMA3D can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Secreted
Secreted: Yes
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.3
Highest tissue expression: 38 nTPM

Expression across tissuesHPA

Tissue

spleen: 38 nTPM
thyroid gland: 33 nTPM
prostate: 6.4 nTPM
blood vessel: 5 nTPM
breast: 4.7 nTPM
cervix: 4.3 nTPM

Single-cell type

lymphatic endothelial cells: 477 nCPM
leydig cells: 253 nCPM
prostatic glandular cells: 245 nCPM
early spermatids: 213 nCPM
mesothelial cells: 208 nCPM
peritubular myoid cells: 190 nCPM

Immune cell

naive B-cell: 0.2 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM

Brain region

midbrain: 16 nTPM
cerebral cortex: 12 nTPM
amygdala: 12 nTPM
hypothalamus: 11 nTPM
white matter: 7.6 nTPM
spinal cord: 7.5 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SEMA3D.

Disease | GeneticClinVar

1 pathogenic / likely-pathogenic of 286 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Progressive sensorineural hearing impairment
SEMA3D-related disorder

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.66
gnomAD pLI: 0
gnomAD missense Z: 0.76
DepMap mean gene effect: -0.01
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads SEMA3D as an antibody target. Whether an autoantibody or antibody against SEMA3D could matter depends on whether native SEMA3D is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SEMA3D is annotated as secreted, so native SEMA3D circulates and is directly accessible to antibodies. Secreted and cell-surface proteins are the autoantibody targets most likely to act like drugs, blocking or depleting the native protein.

Annotation status

The present source text does not explicitly label SEMA3D as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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