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SEMA7A

semaphorin 7A (John Milton Hagen blood group), the group of Immunoglobulin like domain containing|Semaphorins|CD molecules|MicroRNA protein coding host genes|Blood group antigens

Basic information

Region (hg38): 15:74409288-74433958

Previous symbols: [ "SEMAL" ]

Links

ENSG00000138623NCBI:8482OMIM:607961HGNC:10741Uniprot:O75326AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cholestasis, progressive familial intrahepatic 11; Blood group, John Milton HagenBG/ARGastrointestinal; HematologicIndividuals with Cholestasis, progressive familial intrahepatic 11 may benefit from medical management (eg, with ursodeoxycholic acid or glutathione); Variants associated with a blood group may be important in specific situations (eg, related to transfusion)Gastrointestinal; Hematologic17207242; 20854351; 34585848

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SEMA7A gene.

  • Inborn genetic diseases (20 variants)
  • not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SEMA7A 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
1
clinvar
1
clinvar
2
missense
17
clinvar
4
clinvar
1
clinvar
22
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 17 5 2

Variants in SEMA7A

This is a list of pathogenic ClinVar variants found in the SEMA7A region.

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

Position Type Phenotype Significance ClinVar
15-74410628-T-G not specified Uncertain significance (Feb 05, 2024)3159933
15-74410662-C-A not specified Uncertain significance (Sep 27, 2021)2252451
15-74410681-G-A SEMA7A-related condition Benign (Oct 24, 2019)3059310
15-74410713-C-T Uncertain significance (Sep 01, 2023)2645539
15-74410724-C-T not specified Uncertain significance (Dec 19, 2023)3159932
15-74410893-G-A not specified Uncertain significance (Sep 16, 2021)2249860
15-74411329-G-A not specified Likely benign (Mar 07, 2024)3233584
15-74411560-C-T not specified Uncertain significance (Dec 14, 2023)3159931
15-74411584-G-A not specified Uncertain significance (Jan 03, 2024)3159930
15-74411588-T-C SEMA7A-related condition Benign (Oct 17, 2019)3060979
15-74411642-G-A SEMA7A-related condition Benign (Aug 20, 2019)3042116
15-74411888-C-G not specified Likely benign (Oct 12, 2022)2318638
15-74411901-G-A not specified Uncertain significance (Oct 25, 2022)2318784
15-74411925-C-T not specified Likely benign (Mar 22, 2022)2392590
15-74411926-G-A John Milton Hagen blood group system Affects (Jan 01, 2007)35579
15-74411928-C-T John Milton Hagen blood group system Affects (Jan 01, 2007)35578
15-74411970-T-C not specified Uncertain significance (Dec 21, 2023)3159928
15-74411983-G-A not specified Likely benign (Jan 11, 2023)2460653
15-74414597-C-A not specified Uncertain significance (Feb 27, 2024)3159927
15-74414602-G-A SEMA7A-related condition Benign (Oct 24, 2019)3059177
15-74414645-G-A not specified Uncertain significance (Jul 12, 2023)2611538
15-74414660-A-G not specified Uncertain significance (Dec 03, 2021)2263615
15-74414831-C-T SEMA7A-related condition Benign (Jun 12, 2019)3033564
15-74414851-G-A not specified Uncertain significance (Jun 06, 2023)2557213
15-74414864-T-C not specified Likely benign (Oct 05, 2021)2391380

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SEMA7Aprotein_codingprotein_codingENST00000261918 1425179
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1800.8201257190231257420.0000915
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.842963990.7410.00002574314
Missense in Polyphen68127.210.534531426
Synonymous-0.6891771661.070.00001121329
Loss of Function4.01832.80.2440.00000158359

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002390.000239
Ashkenazi Jewish0.0003000.000198
East Asian0.00005470.0000544
Finnish0.00004630.0000462
European (Non-Finnish)0.0001060.0000879
Middle Eastern0.00005470.0000544
South Asian0.00003270.0000327
Other0.0001650.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Plays an important role in integrin-mediated signaling and functions both in regulating cell migration and immune responses. Promotes formation of focal adhesion complexes, activation of the protein kinase PTK2/FAK1 and subsequent phosphorylation of MAPK1 and MAPK3. Promotes production of proinflammatory cytokines by monocytes and macrophages. Plays an important role in modulating inflammation and T-cell-mediated immune responses. Promotes axon growth in the embryonic olfactory bulb. Promotes attachment, spreading and dendrite outgrowth in melanocytes. {ECO:0000269|PubMed:12879062, ECO:0000269|PubMed:17377534, ECO:0000269|PubMed:17671519}.;
Pathway
Axon guidance - Homo sapiens (human);Developmental Biology;Other semaphorin interactions;Semaphorin interactions;Axon guidance (Consensus)

Recessive Scores

pRec
0.156

Intolerance Scores

loftool
0.653
rvis_EVS
-1.04
rvis_percentile_EVS
7.77

Haploinsufficiency Scores

pHI
0.306
hipred
Y
hipred_score
0.567
ghis
0.661

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.350

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sema7a
Phenotype
nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cellular phenotype;

Gene ontology

Biological process
osteoblast differentiation;neural crest cell migration;inflammatory response;immune response;integrin-mediated signaling pathway;olfactory lobe development;positive regulation of cell migration;positive regulation of axon extension;axon extension;negative regulation of axon extension involved in axon guidance;regulation of inflammatory response;negative chemotaxis;positive regulation of macrophage cytokine production;positive regulation of ERK1 and ERK2 cascade;semaphorin-plexin signaling pathway
Cellular component
extracellular space;plasma membrane;integral component of plasma membrane;external side of plasma membrane;membrane;anchored component of membrane;collagen-containing extracellular matrix
Molecular function
integrin binding;protein binding;semaphorin receptor binding;neuropilin binding;chemorepellent activity