SSUH2

ssu-2 homolog

Basic information

Region (hg38): 3:8619385-8745040

Previous symbols: [ "C3orf32" ]

Links

ENSG00000125046 ∙ NCBI:51066 ∙ OMIM:617479 ∙ HGNC:24809 ∙ Uniprot:Q9Y2M2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• dentin dysplasia type I (Supportive), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SSUH2 gene.

• Inborn genetic diseases (19 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSUH2 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						0
missense			17	1	3	21
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	18	2	3

Variants in SSUH2

This is a list of pathogenic ClinVar variants found in the SSUH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-8619882-A-G		not specified	Uncertain significance (Oct 17, 2023)
3-8619906-A-G		not specified	Uncertain significance (Nov 10, 2022)
3-8620004-A-G		not specified	Uncertain significance (Nov 18, 2022)
3-8623562-C-T		not specified	Uncertain significance (Apr 25, 2022)
3-8623584-C-T		not specified	Uncertain significance (Mar 07, 2024)
3-8623606-C-A		not specified	Uncertain significance (Aug 31, 2022)
3-8623613-G-C		not specified	Uncertain significance (Nov 21, 2022)
3-8623623-T-C		not specified	Uncertain significance (Apr 07, 2023)
3-8623628-C-T		not specified	Uncertain significance (Jan 26, 2022)
3-8625612-C-T		not specified	Likely benign (Sep 16, 2021)
3-8626233-T-G		not specified	Uncertain significance (Jul 12, 2022)
3-8627716-G-A			Benign (Dec 31, 2019)
3-8627734-C-T		not specified	Uncertain significance (Aug 19, 2021)
3-8627752-C-T		not specified	Uncertain significance (Jun 28, 2022)
3-8629675-C-T		not specified	Uncertain significance (Aug 12, 2021)
3-8629678-G-T		not specified	Uncertain significance (Mar 02, 2023)
3-8629704-C-A		not specified	Uncertain significance (Oct 04, 2022)
3-8629704-C-T		not specified	Uncertain significance (May 25, 2022)
3-8629705-G-A		not specified	Uncertain significance (Nov 13, 2023)
3-8630810-C-A		not specified	Uncertain significance (Jun 21, 2022)
3-8630810-C-T		not specified	Uncertain significance (Jun 03, 2022)
3-8630818-G-A		not specified	Uncertain significance (Oct 03, 2022)
3-8630881-T-TC			Likely benign (Dec 31, 2019)
3-8630918-C-A		not specified	Uncertain significance (Dec 06, 2021)
3-8633733-C-T		not specified	Uncertain significance (Jun 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSUH2	protein_coding	protein_coding	ENST00000544814	12	125641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.99e-10	0.335	125713	0	34	125747	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.441	235	217	1.08	0.0000132	2431
Missense in Polyphen		67	63.499	1.0551		799
Synonymous	-2.11	109	84.3	1.29	0.00000515	706
Loss of Function	0.912	17	21.6	0.788	0.00000106	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000462	0.000456
Ashkenazi Jewish	0.00	0.00
East Asian	0.000171	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000146	0.000141
Middle Eastern	0.000171	0.000163
South Asian	0.000164	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in odontogenesis. {ECO:0000269|PubMed:27680507}.

Intolerance Scores

• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.96

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.170

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ssu2
• Phenotype: skeleton phenotype; craniofacial phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: ssuh2rs1
• Affected structure: ceratobranchial 5 tooth
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: odontogenesis
• Cellular component: nucleus;cytoplasm