SHOX2

short stature homeobox 2, the group of PRD class homeoboxes and pseudogenes

Basic information

Region (hg38): 3:158095905-158106420

Links

ENSG00000168779 ∙ NCBI:6474 ∙ OMIM:602504 ∙ HGNC:10854 ∙ Uniprot:O60902 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
• atrial fibrillation (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SHOX2 gene.

• not_specified (59 variants)
• not_provided (7 variants)
• SHOX2-related_disorder (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SHOX2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001163678.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	5	1	7
missense			53	2		55
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	54	7	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SHOX2	protein_coding	protein_coding	ENST00000389589	6	9345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125741	0	6	125747	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0998	196	192	1.02	0.00000879	2243
Missense in Polyphen		72	92.733	0.77642		1106
Synonymous	-1.38	104	87.6	1.19	0.00000430	758
Loss of Function	1.99	5	12.7	0.395	5.67e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000128	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000183	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a growth regulator and have a role in specifying neural systems involved in processing somatosensory information, as well as in face and body structure formation.

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.127
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: shox2
• Affected structure: sinus venosus
• Phenotype tag: abnormal
• Phenotype quality: hypoplastic

Gene ontology

• Biological process: skeletal system development;osteoblast differentiation;positive regulation of mesenchymal cell proliferation;chondrocyte development;heart valve development;cardiac atrium morphogenesis;regulation of transcription by RNA polymerase II;nervous system development;heart development;regulation of chondrocyte differentiation;embryonic forelimb morphogenesis;positive regulation of smoothened signaling pathway;embryonic digestive tract morphogenesis;positive regulation of skeletal muscle fiber development;positive regulation of axonogenesis;embryonic skeletal joint morphogenesis;cartilage development involved in endochondral bone morphogenesis;muscle tissue morphogenesis;regulation of branching morphogenesis of a nerve
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;sequence-specific DNA binding