CSMD1

CUB and Sushi multiple domains 1, the group of Protein phosphatase 1 regulatory subunits|Complement system regulators and receptors|Sushi domain containing

Basic information

Region (hg38): 8:2935353-4994972

Links

ENSG00000183117 ∙ NCBI:64478 ∙ OMIM:608397 ∙ HGNC:14026 ∙ Uniprot:Q96PZ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSMD1 gene.

• not_specified (676 variants)
• not_provided (176 variants)
• CSMD1-related_disorder (101 variants)
• Cerebellar_ataxia (1 variants)
• Autism_spectrum_disorder (1 variants)
• Large_for_gestational_age (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSMD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033225.6. 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				83	40	123
missense		1	706	26	11	744
nonsense			2			2
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)			2			2
Total	0	1	711	109	51

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSMD1	protein_coding	protein_coding	ENST00000537824	70	2059620

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.37e-10	125645	0	51	125696	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-6.87	2787	1.94e+3	1.44	0.000112	23041
Missense in Polyphen		1120	959.08	1.1678		11311
Synonymous	-16.5	1395	801	1.74	0.0000557	6770
Loss of Function	10.4	27	177	0.153	0.00000922	2109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000788	0.000726
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000110	0.000109
Finnish	0.0000493	0.0000462
European (Non-Finnish)	0.000203	0.000185
Middle Eastern	0.000110	0.000109
South Asian	0.000298	0.000261
Other	0.000181	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential suppressor of squamous cell carcinomas.

Recessive Scores

• pRec: 0.124

Intolerance Scores

• rvis_EVS: -7.11
• rvis_percentile_EVS: 0.02

Haploinsufficiency Scores

• pHI: 0.210
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.746

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csmd1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: startle response;glucose homeostasis
• Cellular component: integral component of membrane