SECISBP2L

protein-coding

SECIS binding protein 2 like

Gene summary

Enables RNA binding activity. Predicted to be involved in selenocysteine incorporation. Predicted to be part of ribonucleoprotein complex. Predicted to be active in mitochondrion. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001193489.2

Inheritance

—

ClinVar variants

U:128B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr15:48,988,476-49,046,447

External References & Databases

Ensembl (ENSG00000138593)

Transcript & Mutation Effects

hg38 • Region Span ~58.0 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 SECISBP2L variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 122

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001193489.2. 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			1 clinvar	3 clinvar		4
missense			123 clinvar	3 clinvar		126
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	128	6	0	134

Loading ClinVar variants...

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_001193489.2	RefSeq	NP_001180418.1	18	MANE Select
ENST00000559471.6	Ensembl	ENSP00000453854.1	18	MANE Select
NM_014701.4	RefSeq	NP_055516.2	17	Standard
ENST00000261847.7	Ensembl	ENSP00000261847.3	17	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

selenocysteine incorporation

Molecular Function

RNA binding
mRNA 3'-UTR binding
protein binding
selenocysteine insertion sequence binding
ribonucleoprotein complex binding

Cellular Component

ribonucleoprotein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000559471
Coding exons: 18
Length: 58088
Individuals with no LoFs: 125721
Homozygous LoFs: 0
Heterozygous LoFs: 27
Defined: 125748
p: 0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.53	455	557	0.817	0.0000271	7246
Missense (PolyPhen)		149	241.77	0.6163		2984
Synonymous	-0.186	196	193	1.02	0.00000943	2078
Loss of Function	5.14	12	52.0	0.231	0.00000278	654

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds SECIS (Sec insertion sequence) elements present on selenocysteine (Sec) protein mRNAs, but does not promote Sec incorporation into selenoproteins in vitro.;

Intolerance Scores

LoFtool: 0.242
RVIS EVS: -0.93
RVIS percentile EVS: 9.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.141

Gene Damage Prediction

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