STEEP1

STING1 ER exit protein 1, the group of Spliceosomal P complex|Spliceosomal C complex

Basic information

Region (hg38): X:119538149-119565409

Previous symbols: [ "CXorf56" ]

Links

ENSG00000018610 ∙ NCBI:63932 ∙ OMIM:301012 ∙ HGNC:26239 ∙ Uniprot:Q9H5V9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, X-linked 107 (Limited), mode of inheritance: XL
• X-linked syndromic intellectual disability (Limited), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked, 107	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic	29374277

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STEEP1 gene.

• Intellectual disability, X-linked 107 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STEEP1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			6			6
nonsense						0
start loss						0
frameshift		2	1			3
inframe indel	1					1
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding					1	1
Total	1	2	7	0	2

Variants in STEEP1

This is a list of pathogenic ClinVar variants found in the STEEP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-119539766-C-T			Likely benign (Jul 01, 2024)
X-119541336-G-A		Intellectual disability, X-linked 107	Pathogenic (-)
X-119541341-C-T		Intellectual disability, X-linked 107	Uncertain significance (Jul 17, 2023)
X-119542509-T-G			Uncertain significance (Jul 14, 2020)
X-119542514-CTCCTCT-C		Intellectual disability, X-linked 107	Pathogenic (Feb 05, 2020)
X-119542524-T-C		Intellectual disability, X-linked 107	Uncertain significance (Nov 24, 2023)
X-119542533-A-G			Uncertain significance (Mar 27, 2019)
X-119544385-T-C			Uncertain significance (Mar 22, 2022)
X-119544401-G-A		Intellectual disability, X-linked 107	Benign (Jul 30, 2021)
X-119544416-G-C			Likely benign (Jul 01, 2024)
X-119544421-C-T			Uncertain significance (Jun 14, 2023)
X-119544489-C-T		Intellectual disability, X-linked 107	Uncertain significance (Dec 21, 2023)
X-119545508-C-T			Uncertain significance (Nov 01, 2023)
X-119560279-CAT-C		Intellectual disability, X-linked 107	Uncertain significance (Aug 24, 2022)
X-119560341-G-C		Intellectual disability, X-linked 107	Uncertain significance (Dec 12, 2018)
X-119560346-C-T			Uncertain significance (May 22, 2024)
X-119560346-CG-C		Intellectual disability, X-linked 107	Likely pathogenic (May 23, 2022)
X-119560350-C-CTA		Intellectual disability, X-linked 107	Pathogenic (Sep 25, 2024)
X-119560352-C-A		Intellectual disability, X-linked 107	Uncertain significance (Sep 26, 2019)
X-119565276-AG-A		Intellectual disability, X-linked 107	Likely pathogenic (Jul 26, 2023)
X-119565312-C-A		Intellectual disability, X-linked 107	Uncertain significance (Mar 12, 2020)
X-119565357-A-G		Intellectual disability, X-linked 107	Benign (Jul 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STEEP1	protein_coding	protein_coding	ENST00000371594	7	27286

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.952	0.0478	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.24	30	89.6	0.335	0.00000692	1462
Missense in Polyphen		4	26.477	0.15107		451
Synonymous	1.53	21	32.0	0.655	0.00000233	396
Loss of Function	2.86	0	9.55	0.00	7.60e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Mental retardation, X-linked 107 (MRX107) [MIM:301013]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Intellectual deficiency is the only primary symptom of non-syndromic X-linked mental retardation, while syndromic mental retardation presents with associated physical, neurological and/or psychiatric manifestations. {ECO:0000269|PubMed:29374277}. Note=The disease is caused by mutations affecting the gene represented in this entry. The disease-causing mutation has been identified in one large family as a 2 base pair insertion in CXorf56 exon 2. This variant produces a premature stop codon, leading to nonsense-mediated mRNA decay. {ECO:0000269|PubMed:29374277}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.155
• hipred: Y
• hipred_score: 0.728
• ghis: 0.631

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C330007P06Rik
• Phenotype: growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype

Gene ontology

• Cellular component: nucleus;cytoplasm;cell body