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GeneBe

SDF2L1

stromal cell derived factor 2 like 1

Basic information

Region (hg38): 22:21642301-21644299

Links

ENSG00000128228NCBI:23753OMIM:607551HGNC:10676Uniprot:Q9HCN8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SDF2L1 gene.

  • Inborn genetic diseases (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDF2L1 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
8
clinvar
8
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 8 0 0

Variants in SDF2L1

This is a list of pathogenic ClinVar variants found in the SDF2L1 region.

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

Position Type Phenotype Significance ClinVar
22-21642382-G-C not specified Uncertain significance (Oct 03, 2022)2315788
22-21642383-G-A not specified Uncertain significance (Aug 16, 2021)3158906
22-21642502-C-T not specified Uncertain significance (Dec 21, 2022)2338709
22-21642508-A-G not specified Uncertain significance (Sep 15, 2021)2249597
22-21642866-C-A not specified Uncertain significance (Apr 17, 2023)2515612
22-21643913-A-G not specified Uncertain significance (Jan 12, 2024)3158904
22-21643951-C-T not specified Uncertain significance (Dec 22, 2023)3158905
22-21643990-C-T not specified Uncertain significance (Jan 29, 2024)3158907
22-21644021-T-C not specified Uncertain significance (Sep 09, 2021)2372441
22-21644056-C-T not specified Uncertain significance (Jan 06, 2023)2470324
22-21644133-C-G not specified Uncertain significance (Mar 01, 2024)3158908
22-21644152-T-C not specified Uncertain significance (May 31, 2023)2554453
22-21644156-C-T not specified Uncertain significance (May 01, 2023)2551011

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SDF2L1protein_codingprotein_codingENST00000248958 32038
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.1900.766125727051257320.0000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.39781210.6440.000006721388
Missense in Polyphen4261.2940.68522673
Synonymous0.7394855.00.8730.00000336462
Loss of Function1.6726.640.3012.86e-777

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001230.000123
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00001770.0000176
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Pathway
Ibuprofen Action Pathway;Phenytoin (Antiarrhythmic) Action Pathway;Ibuprofen Metabolism Pathway;Morphine Metabolism Pathway;Irinotecan Action Pathway;Morphine Action Pathway;Etoposide Action Pathway;Sorafenib Metabolism Pathway;Acetaminophen Metabolism Pathway;Vitamin A Deficiency;Irinotecan Metabolism Pathway;Etoposide Metabolism Pathway;Retinol Metabolism (Consensus)

Recessive Scores

pRec
0.125

Haploinsufficiency Scores

pHI
0.190
hipred
Y
hipred_score
0.573
ghis
0.405

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
1.00

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sdf2l1
Phenotype

Gene ontology

Biological process
regulation of apoptotic process;ER-associated misfolded protein catabolic process
Cellular component
endoplasmic reticulum lumen;membrane;endoplasmic reticulum chaperone complex
Molecular function
chaperone binding;ATPase binding;misfolded protein binding