SPRED3

protein-coding

sprouty related EVH1 domain containing 3

Gene summary

This gene encodes a protein with a C-terminal Sprouty-like cysteine-rich domain (SRY) and an N-terminal Ena/Vasodilator-stimulated phosphoprotein (VASP) homology-1 (EVH-1) domain. The encoded protein is a member of a family of proteins that negatively regulates mitogen-activated protein (MAP) kinase signaling, particularly during organogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]

MANE transcript

NM_001394336.1

Inheritance

—

ClinVar variants

U:71B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr19:38,388,421-38,399,587

External References & Databases

Ensembl (ENSG00000188766)

Transcript & Mutation Effects

hg38 • Region Span ~11.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPRED3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 69

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001394336.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			70 clinvar			70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	71	0	1	72

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001394336.1	RefSeq	NP_001381265.1	5	MANE Select
ENST00000691638.1	Ensembl	ENSP00000510478.1	5	MANE Select
NM_001042522.3	RefSeq	NP_001035987.1	5	Standard
NM_001394337.1	RefSeq	NP_001381266.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
Regulation of RAS by GAPs
RAF/MAP kinase cascade
MAPK1/MAPK3 signaling
MAPK family signaling cascades

Biological Process

multicellular organism development
regulation of signal transduction

Cellular Component

membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000338502
Coding exons: 5
Length: 7821
Individuals with no LoFs: 124782
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 124788
p: 0.0000240

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.43	122	175	0.695	0.0000113	2473
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Tyrosine kinase substrate that inhibits growth-factor- mediated activation of MAP kinase. {ECO:0000250}.;

Recessive Scores

pRec: 0.0814

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.626

Gene Damage Prediction

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