SPRED3

sprouty related EVH1 domain containing 3

Basic information

Region (hg38): 19:38388421-38399587

Links

ENSG00000188766 ∙ NCBI:399473 ∙ OMIM:609293 ∙ HGNC:31041 ∙ Uniprot:Q2MJR0 ∙ 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 SPRED3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRED3 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			40			40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	0	1

Variants in SPRED3

This is a list of pathogenic ClinVar variants found in the SPRED3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-38390376-G-T		not specified	Uncertain significance (Feb 19, 2025)
19-38390394-T-A		not specified	Uncertain significance (Dec 16, 2024)
19-38390408-G-A		not specified	Uncertain significance (May 31, 2023)
19-38390424-G-T		not specified	Uncertain significance (Oct 06, 2024)
19-38390426-G-T		not specified	Uncertain significance (Mar 25, 2024)
19-38390427-G-A		not specified	Uncertain significance (Nov 21, 2024)
19-38390427-G-T		not specified	Uncertain significance (Mar 25, 2024)
19-38390433-G-A		not specified	Uncertain significance (Oct 06, 2024)
19-38390433-G-C		not specified	Uncertain significance (Mar 15, 2024)
19-38390455-C-T			Benign (Jun 01, 2018)
19-38390478-A-G		not specified	Uncertain significance (Jul 14, 2024)
19-38392094-C-T		not specified	Uncertain significance (Jun 26, 2024)
19-38394659-A-G		not specified	Uncertain significance (Feb 02, 2024)
19-38394661-T-G		not specified	Uncertain significance (Feb 02, 2024)
19-38394662-C-A		not specified	Uncertain significance (Feb 02, 2024)
19-38394744-C-A		not specified	Uncertain significance (May 15, 2024)
19-38394761-C-A		not specified	Uncertain significance (Apr 08, 2024)
19-38394764-A-G		not specified	Uncertain significance (Dec 14, 2024)
19-38394767-G-T		not specified	Uncertain significance (Mar 28, 2023)
19-38394772-C-T		not specified	Uncertain significance (Feb 27, 2023)
19-38394776-C-T		not specified	Uncertain significance (Jan 20, 2025)
19-38394781-G-A		not specified	Uncertain significance (Aug 17, 2022)
19-38395505-C-T		not specified	Uncertain significance (Dec 02, 2021)
19-38395546-G-A		not specified	Uncertain significance (Mar 19, 2024)
19-38395567-G-A		not specified	Uncertain significance (May 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRED3	protein_coding	protein_coding	ENST00000338502	5	7821

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.212	0.780	124782	0	6	124788	0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	122	175	0.695	0.0000113	2473
Missense in Polyphen		42	81.836	0.51322		1242
Synonymous	0.819	71	80.3	0.884	0.00000553	918
Loss of Function	2.29	3	11.3	0.266	6.15e-7	139

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tyrosine kinase substrate that inhibits growth-factor- mediated activation of MAP kinase. {ECO:0000250}.
• Pathway: Signal Transduction;Regulation of RAS by GAPs;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades (Consensus)

Recessive Scores

• pRec: 0.0814

Haploinsufficiency Scores

• pHI: 0.183
• hipred: Y
• hipred_score: 0.678
• ghis: 0.424

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.626

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Spred3

Gene ontology

• Biological process: multicellular organism development;regulation of signal transduction
• Cellular component: membrane