SUSD2

sushi domain containing 2, the group of Sushi domain containing

Basic information

Region (hg38): 22:24181487-24189106

Links

ENSG00000099994 ∙ NCBI:56241 ∙ OMIM:615825 ∙ HGNC:30667 ∙ Uniprot:Q9UGT4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SUSD2 gene.

• not_specified (160 variants)
• not_provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUSD2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000019601.4. 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				7	1	8
missense			147	12	3	162
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	147	19	4

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUSD2	protein_coding	protein_coding	ENST00000358321	15	7852

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.81e-21	0.0209	125414	1	330	125745	0.00132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.111	526	533	0.986	0.0000361	5238
Missense in Polyphen		169	179.64	0.94077		1982
Synonymous	-0.673	254	241	1.06	0.0000185	1672
Loss of Function	0.980	36	42.9	0.839	0.00000239	404

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00843	0.00835
Ashkenazi Jewish	0.00	0.00
East Asian	0.00115	0.00114
Finnish	0.00	0.00
European (Non-Finnish)	0.000630	0.000615
Middle Eastern	0.00115	0.00114
South Asian	0.00138	0.00137
Other	0.00131	0.00130

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a cytokine receptor for C10ORF99. May be a tumor suppressor; together with C10ORF99 has a growth inhibitory effect on colon cancer cells which includes G1 cell cycle arrest (PubMed:25351403). May play a role in breast tumorigenesis (PubMed:23131994). {ECO:0000269|PubMed:23131994, ECO:0000269|PubMed:25351403}.

Recessive Scores

• pRec: 0.0883

Intolerance Scores

• loftool: 0.890
• rvis_EVS: -1.07
• rvis_percentile_EVS: 7.35

Haploinsufficiency Scores

• pHI: 0.150
• hipred: N
• hipred_score: 0.267
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.824

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Susd2

Gene ontology

• Biological process: receptor-mediated endocytosis;immune response;negative regulation of cell division;negative regulation of cell cycle G1/S phase transition
• Cellular component: plasma membrane;integral component of membrane;extracellular exosome
• Molecular function: scavenger receptor activity;protein binding;polysaccharide binding