SUSD1

sushi domain containing 1, the group of Sushi domain containing

Basic information

Region (hg38): 9:112040783-112175297

Links

ENSG00000106868 ∙ NCBI:64420 ∙ ∙ HGNC:25413 ∙ Uniprot:Q6UWL2 ∙ 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 SUSD1 gene.

• not_specified (90 variants)
• not_provided (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUSD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022486.5. 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				4	3	7
missense			83	9	2	94
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	83	13	5

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUSD1	protein_coding	protein_coding	ENST00000374270	16	134624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.17e-13	0.831	125599	1	147	125747	0.000589

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	349	408	0.856	0.0000220	4841
Missense in Polyphen		108	128.83	0.83834		1559
Synonymous	-0.167	159	156	1.02	0.00000910	1484
Loss of Function	1.89	26	38.7	0.671	0.00000197	482

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000590	0.000589
Middle Eastern	0.000272	0.000272
South Asian	0.00147	0.00137
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0828

Intolerance Scores

• loftool: 0.485
• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.79

Haploinsufficiency Scores

• pHI: 0.0829
• hipred: N
• hipred_score: 0.145
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.230

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Susd1

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: calcium ion binding