SDF4

stromal cell derived factor 4, the group of CREC family

Basic information

Region (hg38): 1:1216931-1232031

Links

ENSG00000078808 ∙ NCBI:51150 ∙ OMIM:614282 ∙ HGNC:24188 ∙ Uniprot:Q9BRK5 ∙ 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 SDF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SDF4 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	1
missense			27	2		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	29	2	1

Variants in SDF4

This is a list of pathogenic ClinVar variants found in the SDF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-1217537-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-1217562-T-C		not specified	Uncertain significance (Mar 23, 2022)
1-1217591-T-C		not specified	Uncertain significance (Mar 19, 2024)
1-1217660-T-C		not specified	Uncertain significance (Apr 23, 2024)
1-1218472-C-T		not specified	Uncertain significance (Dec 16, 2023)
1-1218484-C-T		not specified	Uncertain significance (Apr 05, 2023)
1-1218550-T-C		not specified	Uncertain significance (Aug 30, 2021)
1-1218551-G-C		not specified	Uncertain significance (Mar 16, 2022)
1-1218613-G-A		not specified	Uncertain significance (Dec 15, 2022)
1-1218625-C-T		not specified	Uncertain significance (Jun 17, 2024)
1-1223250-C-T		not specified	Uncertain significance (Mar 18, 2024)
1-1223276-C-T		not specified	Likely benign (Jun 01, 2023)
1-1223280-T-C		not specified	Uncertain significance (Mar 07, 2024)
1-1223292-C-T		not specified	Uncertain significance (Dec 07, 2021)
1-1223301-C-T		not specified	Uncertain significance (May 02, 2024)
1-1223306-T-C		not specified	Uncertain significance (Dec 02, 2022)
1-1223309-C-T		not specified	Uncertain significance (Sep 01, 2021)
1-1223318-G-A		not specified	Uncertain significance (Aug 17, 2022)
1-1223336-T-C		not specified	Uncertain significance (Apr 28, 2022)
1-1223352-C-A		not specified	Uncertain significance (Oct 10, 2023)
1-1223855-C-T		not specified	Uncertain significance (Mar 30, 2024)
1-1223856-G-A		not specified	Uncertain significance (Nov 14, 2023)
1-1223859-A-G		not specified	Uncertain significance (Jan 31, 2024)
1-1223898-C-T		not specified	Uncertain significance (Apr 17, 2023)
1-1223943-T-C		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SDF4	protein_coding	protein_coding	ENST00000360001	6	15124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00910	0.980	125703	0	21	125724	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.553	227	252	0.902	0.0000171	2434
Missense in Polyphen		65	87.206	0.74536		805
Synonymous	-0.460	121	115	1.05	0.00000963	656
Loss of Function	2.24	6	15.5	0.387	7.28e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000981	0.0000967
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate calcium-dependent activities in the endoplasmic reticulum lumen or post-ER compartment. {ECO:0000250}.

Recessive Scores

• pRec: 0.355

Intolerance Scores

• loftool: 0.585
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.14

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.310
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sdf4

Zebrafish Information Network

• Gene name: sdf4
• Affected structure: dorsal longitudinal anastomotic vessel
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: UV protection;calcium ion regulated exocytosis;cerebellum development;fat cell differentiation;response to ethanol;zymogen granule exocytosis
• Cellular component: cytoplasm;late endosome;endoplasmic reticulum;Golgi apparatus;Golgi lumen;plasma membrane;membrane;bleb;extracellular exosome
• Molecular function: calcium ion binding;identical protein binding