SPATS2

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			69 clinvar	2 clinvar	1 clinvar	72
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	73	2	1	76

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 79 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_023071.4	RefSeq	NP_075559.2	12	MANE Select
ENST00000552918.6	Ensembl	ENSP00000447947.2	12	MANE Select
NM_001293285.2	RefSeq	NP_001280214.1	12	Standard
NM_001293286.2	RefSeq	NP_001280215.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding

Cellular Component

cytoplasm
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000553127
Coding exons: 12
Length: 160839
Individuals with no LoFs: 125174
Homozygous LoFs: 2
Heterozygous LoFs: 572
Defined: 125748
p: 0.00229

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.796	258	297	0.870	0.0000156	3583
Missense (PolyPhen)		85	111.97	0.75917		1368
Synonymous	0.636	99	107	0.922	0.00000586	1047
Loss of Function	4.27	4	28.7	0.139	0.00000172	333

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0.0019	0.0019	notable
East Asian	0.000054	0.000054	rare
Finnish	0.011	0.011	notable
European (Non-Finnish)	0.0024	0.0024	notable
South Asian	0.00049	0.00049	rare
Other	0.0024	0.0024	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0849

Intolerance Scores

LoFtool: 0.132
RVIS EVS: -0.27
RVIS percentile EVS: 34.71

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.182

Gene Damage Prediction

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