CSMD3

CUB and Sushi multiple domains 3, the group of Sushi domain containing|Complement system regulators and receptors

Basic information

Region (hg38): 8:112222927-113436939

Links

ENSG00000164796 ∙ NCBI:114788 ∙ OMIM:608399 ∙ HGNC:19291 ∙ Uniprot:Q7Z407 ∙ 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 CSMD3 gene.

• Inborn genetic diseases (101 variants)
• not provided (41 variants)
• CSMD3-related condition (3 variants)
• CSMD3-associated Hirschsprung disease (1 variants)
• Hereditary breast ovarian cancer syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSMD3 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			1	10	12	23
missense			107	5	6	118
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1	1	2
non coding				2		2
Total	0	0	109	17	18

Variants in CSMD3

This is a list of pathogenic ClinVar variants found in the CSMD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-112224816-C-T		CSMD3-related disorder	Benign (Dec 20, 2019)
8-112224868-G-A		not specified	Uncertain significance (Dec 02, 2021)
8-112228792-A-G		not specified	Uncertain significance (Oct 12, 2021)
8-112228823-T-G		not specified	Uncertain significance (Dec 09, 2023)
8-112228837-C-T		not specified	Uncertain significance (Dec 14, 2021)
8-112228859-T-G		CSMD3-related disorder	Benign (Oct 17, 2019)
8-112231559-C-T		not specified	Uncertain significance (Nov 07, 2022)
8-112234358-T-C			Likely benign (Oct 01, 2023)
8-112234431-A-G		CSMD3-related disorder	Benign (Sep 30, 2019)
8-112234441-C-T		not specified	Likely benign (Jul 20, 2021)
8-112237207-A-C		not specified	Uncertain significance (Oct 27, 2022)
8-112237208-T-C		not specified	Uncertain significance (Sep 06, 2022)
8-112237229-C-T		not specified	Uncertain significance (Feb 09, 2022)
8-112237297-A-G		not specified	Uncertain significance (May 17, 2023)
8-112241725-A-G		CSMD3-related disorder	Benign (Apr 16, 2019)
8-112244433-A-C		not specified	Uncertain significance (Jul 20, 2021)
8-112244475-C-G		not specified	Uncertain significance (Feb 22, 2023)
8-112244519-T-A		not specified	Uncertain significance (Jul 25, 2023)
8-112244549-G-A		not specified	Uncertain significance (Nov 06, 2023)
8-112244557-C-G		not specified	Uncertain significance (Aug 15, 2023)
8-112247099-T-C		CSMD3-related disorder	Likely benign (Feb 25, 2019)
8-112247125-T-C		not specified	Uncertain significance (Nov 08, 2022)
8-112247135-T-C		CSMD3-related disorder	Likely benign (Mar 28, 2019)
8-112254262-G-A		CSMD3-related disorder	Benign (May 03, 2019)
8-112254270-T-C		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSMD3	protein_coding	protein_coding	ENST00000297405	71	1214172

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0571	0.943	125672	0	76	125748	0.000302

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	1813	1.95e+3	0.927	0.000101	24216
Missense in Polyphen		710	868.58	0.81743		10769
Synonymous	-2.61	760	674	1.13	0.0000349	7132
Loss of Function	9.96	46	197	0.234	0.0000106	2374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000594	0.000594
Ashkenazi Jewish	0.000794	0.000794
East Asian	0.000218	0.000217
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000300	0.000299
Middle Eastern	0.000218	0.000217
South Asian	0.000327	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in dendrite development. {ECO:0000250|UniProtKB:Q80T79}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.585
• rvis_EVS: -3.49
• rvis_percentile_EVS: 0.35

Haploinsufficiency Scores

• pHI: 0.399
• hipred: Y
• hipred_score: 0.649
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.758

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csmd3

Gene ontology

• Biological process: regulation of dendrite development
• Cellular component: plasma membrane;integral component of membrane