SUCO

SUN domain containing ossification factor

Basic information

Region (hg38): 1:172532349-172611833

Previous symbols: [ "C1orf9" ]

Links

ENSG00000094975 ∙ NCBI:51430 ∙ OMIM:619434 ∙ HGNC:1240 ∙ Uniprot:Q9UBS9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• temporal lobe epilepsy (Limited), mode of inheritance: AD
• osteogenesis imperfecta (Moderate), mode of inheritance: AR

ClinVar

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

• not_provided (447 variants)
• not_specified (154 variants)
• SUCO-related_disorder (11 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUCO gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014283.5. 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	97	6	104
missense			318	12	4	334
nonsense			2			2
start loss						0
frameshift			5			5
splice donor/acceptor (+/-2bp)			3	1		4
Total	0	0	329	110	10

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUCO	protein_coding	protein_coding	ENST00000263688	24	79483

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125573	1	169	125743	0.000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	555	631	0.879	0.0000311	8170
Missense in Polyphen		118	180.76	0.65279		2379
Synonymous	0.00276	222	222	1.00	0.0000112	2377
Loss of Function	6.04	12	64.2	0.187	0.00000329	860

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000196	0.000189
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.000141	0.000139
European (Non-Finnish)	0.000242	0.000237
Middle Eastern	0.000114	0.000109
South Asian	0.00461	0.00429
Other	0.000675	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for bone modeling during late embryogenesis. Regulates type I collagen synthesis in osteoblasts during their postnatal maturation (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.235

Intolerance Scores

• rvis_EVS: -1.24
• rvis_percentile_EVS: 5.52

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H

Gene Damage Prediction

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

Gene ontology

• Biological process: ossification;multicellular organism development;positive regulation of collagen biosynthetic process;protein folding in endoplasmic reticulum;positive regulation of osteoblast differentiation;regulation of bone remodeling
• Cellular component: cytoplasm;rough endoplasmic reticulum;membrane;integral component of membrane;rough endoplasmic reticulum membrane