SUSD5

sushi domain containing 5, the group of Sushi domain containing

Basic information

Region (hg38): 3:33150042-33218810

Links

ENSG00000173705 ∙ NCBI:26032 ∙ OMIM:619917 ∙ HGNC:29061 ∙ Uniprot:O60279 ∙ 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 SUSD5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUSD5 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				2		2
missense			36	4		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	6	0

Variants in SUSD5

This is a list of pathogenic ClinVar variants found in the SUSD5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-33152779-C-T		not specified	Uncertain significance (Dec 03, 2021)
3-33152780-G-C		not specified	Uncertain significance (Jul 20, 2021)
3-33152848-A-G		not specified	Uncertain significance (Oct 29, 2021)
3-33152905-A-C		not specified	Uncertain significance (Jan 22, 2024)
3-33152936-C-T		not specified	Uncertain significance (Oct 04, 2022)
3-33152938-T-C		not specified	Likely benign (Dec 06, 2021)
3-33152990-C-T		not specified	Uncertain significance (Mar 04, 2024)
3-33153008-A-G		not specified	Likely benign (Mar 29, 2023)
3-33153059-T-C		not specified	Uncertain significance (Jan 03, 2024)
3-33153087-C-G		not specified	Uncertain significance (Mar 07, 2023)
3-33153094-G-A		not specified	Uncertain significance (Jan 22, 2024)
3-33153163-A-G		not specified	Uncertain significance (Jun 01, 2023)
3-33153165-C-A		not specified	Uncertain significance (Jan 05, 2022)
3-33153169-T-C		not specified	Uncertain significance (Mar 15, 2024)
3-33153229-T-C		not specified	Uncertain significance (Apr 15, 2024)
3-33153253-A-G		not specified	Uncertain significance (Nov 02, 2023)
3-33153265-T-C		not specified	Uncertain significance (Jan 18, 2022)
3-33153280-G-A		not specified	Uncertain significance (May 21, 2024)
3-33153302-C-A		not specified	Uncertain significance (Dec 06, 2023)
3-33153346-T-C		not specified	Uncertain significance (Jul 27, 2021)
3-33153384-T-G		not specified	Uncertain significance (Jun 16, 2023)
3-33153400-T-C		not specified	Uncertain significance (Aug 12, 2021)
3-33153422-T-G		not specified	Uncertain significance (Jul 30, 2023)
3-33153446-C-T		not specified	Uncertain significance (Jun 07, 2023)
3-33153601-T-C		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUSD5	protein_coding	protein_coding	ENST00000309558	5	69171

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.00e-11	0.0979	124993	0	48	125041	0.000192

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.121	346	352	0.982	0.0000191	4061
Missense in Polyphen		84	92.66	0.90654		1048
Synonymous	0.317	142	147	0.967	0.00000857	1310
Loss of Function	0.366	17	18.7	0.909	7.88e-7	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000844	0.000830
Ashkenazi Jewish	0.00	0.00
East Asian	0.000614	0.000612
Finnish	0.0000928	0.0000928
European (Non-Finnish)	0.000107	0.000106
Middle Eastern	0.000614	0.000612
South Asian	0.0000980	0.0000980
Other	0.000331	0.000328

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0792

Intolerance Scores

• loftool: 0.802
• rvis_EVS: 1.53
• rvis_percentile_EVS: 95.56

Haploinsufficiency Scores

• pHI: 0.226
• hipred: N
• hipred_score: 0.153
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Susd5

Gene ontology

• Biological process: cell adhesion;Notch signaling pathway
• Cellular component: integral component of membrane
• Molecular function: hyaluronic acid binding