SDF2

stromal cell derived factor 2

Basic information

Region (hg38): 17:28648345-28662189

Links

ENSG00000132581 ∙ NCBI:6388 ∙ OMIM:602934 ∙ HGNC:10675 ∙ Uniprot:Q99470 ∙ 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 SDF2 gene.

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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	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)
17-28649090-T-C		not specified	Uncertain significance (Jan 19, 2022)
17-28655334-G-C		not specified	Uncertain significance (Aug 04, 2023)
17-28655384-G-T		not specified	Uncertain significance (Apr 07, 2022)
17-28655390-C-T		not specified	Uncertain significance (Nov 12, 2021)
17-28661818-C-G		not specified	Uncertain significance (Jul 27, 2021)
17-28661845-C-A		not specified	Uncertain significance (Oct 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDF2	protein_coding	protein_coding	ENST00000247020	3	13834

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0264	0.925	125718	0	30	125748	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.647	99	119	0.833	0.00000581	1362
Missense in Polyphen		29	50.607	0.57304		562
Synonymous	-0.239	48	45.9	1.04	0.00000203	437
Loss of Function	1.69	4	9.68	0.413	5.69e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000386	0.000386
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

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

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

Mouse Genome Informatics

• Gene name: Sdf2

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