SUSD5

protein-coding

sushi domain containing 5, the group of Sushi domain containing

Gene summary

Predicted to enable hyaluronic acid binding activity. Predicted to be involved in Notch signaling pathway. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_015551.2

Inheritance

—

ClinVar variants

U:100B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr3:33,150,043-33,218,810

External References & Databases

Ensembl (ENSG00000173705)

Transcript & Mutation Effects

hg38 • Region Span ~68.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SUSD5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 111

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015551.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense			100 clinvar	11 clinvar		111
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	100	14	0	114

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015551.2	RefSeq	NP_056366.1	5	MANE Select
ENST00000309558.8	Ensembl	ENSP00000308727.3	5	MANE Select
ENST00000412539.1	Ensembl	ENSP00000406475.1	4	Standard
ENST00001011571.1	Ensembl	ENSP00000681388.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cell adhesion
Notch signaling pathway

Molecular Function

hyaluronic acid binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000309558
Coding exons: 5
Length: 69171
Individuals with no LoFs: 124993
Homozygous LoFs: 0
Heterozygous LoFs: 48
Defined: 125041
p: 0.000192

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.121	346	352	0.982	0.0000191	4061
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00058	0.00057	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00061	0.00061	rare
Finnish	0.000093	0.000093	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000098	0.000098	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0792

Intolerance Scores

LoFtool: 0.802
RVIS EVS: 1.53
RVIS percentile EVS: 95.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.137

Gene Damage Prediction

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