SPDYE1

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						0
missense			90 clinvar			90
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	90	0	0	90

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001378423.2	RefSeq	NP_001365352.1	7	MANE Select
ENST00000693451.1	Ensembl	ENSP00000509569.1	7	MANE Select
NM_175064.4	RefSeq	NP_778234.2	6	Standard
ENST00000258704.3	Ensembl	ENSP00000258704.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Oocyte meiosis - Homo sapiens (human)
Progesterone-mediated oocyte maturation - Homo sapiens (human)

Molecular Function

protein kinase binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000258704
Coding exons: 6
Length: 9234
Individuals with no LoFs: 125648
Homozygous LoFs: 0
Heterozygous LoFs: 99
Defined: 125747
p: 0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.459	208	190	1.09	0.0000132	2193
Missense (PolyPhen)		46	49.836	0.92302		692
Synonymous	-1.03	83	71.9	1.15	0.00000459	612
Loss of Function	0.337	17	18.6	0.915	0.00000119	199

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00090	0.00084	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00062	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00032	0.00031	rare
South Asian	0.00053	0.00052	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Disease: DISEASE: Note=SPDYE1 is located in the Williams-Beuren syndrome (WBS) critical region. WBS results from a hemizygous deletion of several genes on chromosome 7q11.23, thought to arise as a consequence of unequal crossing over between highly homologous low-copy repeat sequences flanking the deleted region (PubMed:12073013). {ECO:0000269|PubMed:12073013}.;

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0351

Gene Damage Prediction

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