CSMD3

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

Basic information

Region (hg38): 8:112222928-113436939

Links

ENSG00000164796 ∙ NCBI:114788 ∙ OMIM:608399 ∙ HGNC:19291 ∙ Uniprot:Q7Z407 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSMD3 gene.

• not_specified (351 variants)
• CSMD3-related_disorder (68 variants)
• not_provided (42 variants)
• Familial_meningioma (4 variants)
• Pachygyria-intellectual_disability-epilepsy_syndrome (2 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. These statistics are base on transcript: NM_000198123.2. 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			2	25	15	42
missense			367	9	10	386
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	371	34	25

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