SPATS2L

protein-coding

spermatogenesis associated serine rich 2 like

Gene summary

Enables RNA binding activity. Located in cytosol and nucleolus. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001100423.2

Inheritance

—

ClinVar variants

U:95B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.21

Max pathogenic AF

—

Genomic locus

chr2:200,305,881-200,482,264

External References & Databases

Ensembl (ENSG00000196141)

Transcript & Mutation Effects

hg38 • Region Span ~176.4 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 SPATS2L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 86

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001100423.2. 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			4 clinvar			4
missense			86 clinvar	2 clinvar		88
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	95	2	0	97

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 192 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001100423.2	RefSeq	NP_001093893.1	11	MANE Select
ENST00000409140.8	Ensembl	ENSP00000386730.3	11	MANE Select
NM_001100422.1	RefSeq	NP_001093892.1	11	Standard
NM_001100424.1	RefSeq	NP_001093894.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

RNA binding

Cellular Component

nucleus
nucleolus
cytoplasm
cytosol
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358677
Coding exons: 11
Length: 176383
Individuals with no LoFs: 124629
Homozygous LoFs: 0
Heterozygous LoFs: 8
Defined: 124637
p: 0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.31	243	308	0.790	0.0000176	3648
Missense (PolyPhen)		79	128.37	0.61541		1586
Synonymous	0.200	121	124	0.977	0.00000803	1069
Loss of Function	3.62	5	24.2	0.206	0.00000110	325

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000027	0.000027	rare
South Asian	0	0.0	absent
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.0568
RVIS EVS: 0.17
RVIS percentile EVS: 65.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.929

Gene Damage Prediction

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