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): 8:2935352-4994972

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

ClinVar

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

• Inborn genetic diseases (212 variants)
• not provided (167 variants)
• CSMD1-related condition (18 variants)
• not specified (2 variants)
• Large for gestational age (1 variants)
• Cerebellar ataxia (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.

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				48	36	84
missense		1	249	11	12	273
nonsense			1			1
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)			2			2
splice region			2	7	8	17
non coding				5	11	16
Total	0	1	253	64	59

Variants in CSMD1

This is a list of pathogenic ClinVar variants found in the CSMD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-2938592-A-T		not specified	Uncertain significance (Mar 16, 2023)
8-2938631-G-C		not specified	Uncertain significance (Jan 03, 2024)
8-2938673-T-A		CSMD1-related disorder	Uncertain significance (Oct 05, 2022)
8-2938686-C-T		not specified	Uncertain significance (Jul 13, 2021)
8-2938699-G-C		not specified	Uncertain significance (Feb 11, 2022)
8-2938722-T-C		not specified	Uncertain significance (Jul 05, 2023)
8-2938739-C-G		not specified	Uncertain significance (Mar 27, 2023)
8-2938755-C-T			Benign (Feb 10, 2021)
8-2942476-G-T		not specified	Uncertain significance (Jan 02, 2024)
8-2942565-T-A		not specified	Uncertain significance (Mar 01, 2023)
8-2942574-C-T		CSMD1-related disorder	Benign (Mar 05, 2019)
8-2942578-A-T			Uncertain significance (Mar 26, 2021)
8-2942585-T-A		not specified	Uncertain significance (Apr 26, 2023)
8-2942602-G-C		CSMD1-related disorder	Benign (Apr 20, 2021)
8-2942608-T-C		CSMD1-related disorder	Likely benign (Sep 18, 2019)
8-2949338-G-T		not specified	Uncertain significance (Oct 25, 2023)
8-2949343-T-C		not specified	Uncertain significance (Dec 06, 2021)
8-2949363-T-C			Likely benign (Dec 31, 2019)
8-2949370-T-C		not specified	Uncertain significance (Jan 08, 2024)
8-2950230-C-T		CSMD1-related disorder	Uncertain significance (Jul 31, 2023)
8-2950251-T-A		not specified	Uncertain significance (Dec 07, 2023)
8-2950314-G-C			Uncertain significance (Mar 01, 2023)
8-2950341-T-C		not specified	Likely benign (Apr 06, 2022)
8-2951118-C-T			Likely benign (Jan 01, 2023)
8-2951126-G-C		not specified	Uncertain significance (May 17, 2023)

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