SKOR2

protein-coding

SKI family transcriptional corepressor 2, the group of SKI transcriptional corepressors

Gene summary

Enables SMAD binding activity and sequence-specific double-stranded DNA binding activity. Involved in negative regulation of transforming growth factor beta receptor signaling pathway. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001278063.4

Inheritance

ClinVar variants

P:3U:2

Top phenotype

Mild intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.17

Max pathogenic AF

—

Genomic locus

chr18:47,206,169-47,251,660

External References & Databases

Ensembl (ENSG00000215474)

Transcript & Mutation Effects

hg38 • Region Span ~45.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

nervous system disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0005071

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SKOR2 variants in ClinVar

4 Conditions Cataloged

Mild intellectual disabilityTotal: 2

DysarthriaTotal: 2

Gait ataxiaTotal: 2

Valence-Farazi cerebellar ataxia syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001278063.4. 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						0
missense	1 clinvar					1
nonsense	1 clinvar					1
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	3	0	2	0	0	5

Highest pathogenic variant AF is 0.0000066190096

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001278063.4	RefSeq	NP_001264992.1	7	MANE Select
ENST00000425639.3	Ensembl	ENSP00000414750.3	7	MANE Select
NM_001037802.3	RefSeq	NP_001032891.1	3	Standard
ENST00000400404.1	Ensembl	ENSP00000383255.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated
negative regulation of transforming growth factor beta receptor signaling pathway
negative regulation of BMP signaling pathway
negative regulation of cell differentiation
neuron development

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
transcription corepressor activity
SMAD binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000425639
Coding exons: 6
Length: 29262
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.63	193	268	0.720	0.0000133	6335
Missense (PolyPhen)		34	85.595	0.39722		997
Synonymous	-1.09	129	114	1.13	0.00000587	2139
Loss of Function	3.25	3	17.8	0.169	8.53e-7	309

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Exhibits transcriptional repressor activity (By similarity). Acts as a TGF-beta antagonist in the nervous system. {ECO:0000250, ECO:0000269|PubMed:16200078}.;

Essentials

Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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