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

ClinVar

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

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.

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				68	6	74
missense			174	5	7	186
nonsense			2			2
start loss			2			2
frameshift			4			4
inframe indel			2	1		3
splice donor/acceptor (+/-2bp)				1		1
splice region			5	11	2	18
non coding			20	47	6	73
Total	0	0	204	122	19

Variants in SUCO

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

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

Position	Type	Phenotype	Significance	ClinVar
1-172532477-G-C		SUCO-related disorder	Benign (Jan 27, 2020)
1-172532503-T-C		SUCO-related disorder	Benign (Oct 31, 2019)
1-172533172-A-T		SUCO-related disorder	Benign (Nov 14, 2019)
1-172533200-T-C		SUCO-related disorder	Benign (Oct 31, 2019)
1-172533466-G-A			Uncertain significance (Nov 15, 2023)
1-172533467-T-G		not specified	Uncertain significance (Dec 16, 2023)
1-172533477-C-T		SUCO-related disorder	Benign (Jan 29, 2024)
1-172533496-T-C			Uncertain significance (Mar 13, 2022)
1-172533507-C-G			Likely benign (Nov 23, 2022)
1-172533508-GCGA-G			Likely benign (Mar 19, 2023)
1-172533510-G-A			Likely benign (Nov 08, 2022)
1-172533512-C-A			Likely benign (Aug 23, 2022)
1-172533515-C-A			Likely benign (Dec 20, 2022)
1-172551508-A-G			Likely benign (Jan 04, 2024)
1-172551525-C-T		not specified	Uncertain significance (Sep 03, 2023)
1-172551526-G-A			Uncertain significance (Aug 10, 2022)
1-172551530-A-G			Likely benign (Nov 10, 2023)
1-172551538-AAG-A			Uncertain significance (Sep 26, 2021)
1-172551540-G-A			Uncertain significance (Feb 04, 2023)
1-172551552-G-A		SUCO-related disorder	Benign (Jan 02, 2024)
1-172551559-C-T		not specified	Uncertain significance (Jan 16, 2024)
1-172551560-G-A			Likely benign (Dec 18, 2023)
1-172551570-T-C		not specified	Uncertain significance (Feb 21, 2024)
1-172551578-A-T			Uncertain significance (Sep 23, 2023)
1-172551580-A-G		not specified	Conflicting classifications of pathogenicity (Mar 16, 2024)

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
0.975	0.0255	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

Haploinsufficiency Scores

• pHI: 0.0578
• hipred: N
• hipred_score: 0.384
• ghis: 0.563

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

Mouse Genome Informatics

• Gene name: Suco
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; growth/size/body region phenotype; renal/urinary system phenotype; skeleton phenotype; immune system 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); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype

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