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GeneBe

SDF2

stromal cell derived factor 2

Basic information

Region (hg38): 17:28648345-28662189

Links

ENSG00000132581NCBI:6388OMIM:602934HGNC:10675Uniprot:Q99470AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SDF2 gene.

  • Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDF2 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
0
missense
6
clinvar
6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 6 0 0

Variants in SDF2

This is a list of pathogenic ClinVar variants found in the SDF2 region.

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

Position Type Phenotype Significance ClinVar
17-28649045-T-C not specified Uncertain significance (Dec 06, 2021)2265235
17-28649090-T-C not specified Uncertain significance (Jan 19, 2022)2349043
17-28655334-G-C not specified Uncertain significance (Aug 04, 2023)2616139
17-28655384-G-T not specified Uncertain significance (Apr 07, 2022)2281855
17-28655390-C-T not specified Uncertain significance (Nov 12, 2021)2260729
17-28661818-C-G not specified Uncertain significance (Jul 27, 2021)2315265
17-28661845-C-A not specified Uncertain significance (Oct 30, 2023)3158903

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SDF2protein_codingprotein_codingENST00000247020 313834
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.02640.9251257180301257480.000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.647991190.8330.000005811362
Missense in Polyphen2950.6070.57304562
Synonymous-0.2394845.91.040.00000203437
Loss of Function1.6949.680.4135.69e-794

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003860.000386
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.0001230.000123
Middle Eastern0.000.00
South Asian0.00009800.0000980
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.130

Intolerance Scores

loftool
0.416
rvis_EVS
0.33
rvis_percentile_EVS
73.11

Haploinsufficiency Scores

pHI
0.242
hipred
Y
hipred_score
0.591
ghis
0.418

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.758

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sdf2
Phenotype

Gene ontology

Biological process
protein glycosylation;protein O-linked mannosylation;ER-associated misfolded protein catabolic process
Cellular component
extracellular space;endoplasmic reticulum membrane
Molecular function
dolichyl-phosphate-mannose-protein mannosyltransferase activity