SDF2L1

stromal cell derived factor 2 like 1

Basic information

Region (hg38): 22:21642302-21644299

Links

ENSG00000128228 ∙ NCBI:23753 ∙ OMIM:607551 ∙ HGNC:10676 ∙ Uniprot:Q9HCN8 ∙ 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 SDF2L1 gene.

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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	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)
22-21642383-G-A		not specified	Uncertain significance (Aug 16, 2021)
22-21642502-C-T		not specified	Uncertain significance (Dec 21, 2022)
22-21642508-A-G		not specified	Uncertain significance (Sep 15, 2021)
22-21642866-C-A		not specified	Uncertain significance (Apr 17, 2023)
22-21643913-A-G		not specified	Uncertain significance (Jan 12, 2024)
22-21643951-C-T		not specified	Uncertain significance (Dec 22, 2023)
22-21643990-C-T		not specified	Uncertain significance (Jan 29, 2024)
22-21644021-T-C		not specified	Uncertain significance (Sep 09, 2021)
22-21644056-C-T		not specified	Uncertain significance (Jan 06, 2023)
22-21644133-C-G		not specified	Uncertain significance (Mar 01, 2024)
22-21644152-T-C		not specified	Uncertain significance (May 31, 2023)
22-21644156-C-T		not specified	Uncertain significance (May 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDF2L1	protein_coding	protein_coding	ENST00000248958	3	2038

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.190	0.766	125727	0	5	125732	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	78	121	0.644	0.00000672	1388
Missense in Polyphen		42	61.294	0.68522		673
Synonymous	0.739	48	55.0	0.873	0.00000336	462
Loss of Function	1.67	2	6.64	0.301	2.86e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Sdf2l1

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