SUSD2

protein-coding

sushi domain containing 2, the group of Sushi domain containing

Gene summary

Involved in negative regulation of cell cycle G1/S phase transition and negative regulation of cell division. Located in plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_019601.4

Inheritance

—

ClinVar variants

U:176B:24

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.84

Max pathogenic AF

—

Genomic locus

chr22:24,181,487-24,189,106

External References & Databases

Ensembl (ENSG00000099994)

Transcript & Mutation Effects

hg38 • Region Span ~7.6 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 SUSD2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 185

not providedTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_019601.4. 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				7 clinvar	1 clinvar	8
missense			175 clinvar	13 clinvar	3 clinvar	191
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	176	20	4	200

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_019601.4	RefSeq	NP_062547.1	15	MANE Select
ENST00000358321.4	Ensembl	ENSP00000351075.3	15	MANE Select
ENST00000886473.1	Ensembl	ENSP00000556532.1	15	Standard
ENST00000886473.2	Ensembl	ENSP00000556532.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

receptor-mediated endocytosis
immune response
negative regulation of cell division
negative regulation of cell cycle G1/S phase transition

Molecular Function

scavenger receptor activity
protein binding
polysaccharide binding

Cellular Component

plasma membrane
integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358321
Coding exons: 15
Length: 7852
Individuals with no LoFs: 125414
Homozygous LoFs: 1
Heterozygous LoFs: 330
Defined: 125745
p: 0.00132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.111	526	533	0.986	0.0000361	5238
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0054	0.0053	notable
Latino/Admixed American	0.0030	0.0030	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0012	0.0011	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00063	0.00062	rare
South Asian	0.0014	0.0014	notable
Other	0.0013	0.0013	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.824

Gene Damage Prediction

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