DSCAML1

DS cell adhesion molecule like 1, the group of Fibronectin type III domain containing|I-set domain containing|Ig-like cell adhesion molecule family

Basic information

Region (hg38): 11:117427771-117817525

Links

ENSG00000177103 ∙ NCBI:57453 ∙ OMIM:611782 ∙ HGNC:14656 ∙ Uniprot:Q8TD84 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• motor neuron disorder (Limited), mode of inheritance: AR
• retinal disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DSCAML1 gene.

• not provided (957 variants)
• Inborn genetic diseases (77 variants)
• Abnormal brain morphology (1 variants)
• Marfanoid habitus and intellectual disability (1 variants)
• DSCAML1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DSCAML1 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			9	287	33	329
missense			492	7	6	505
nonsense			4			4
start loss			1			1
frameshift			4			4
inframe indel			6	1		7
splice donor/acceptor (+/-2bp)			1			1
splice region			17	22	6	45
non coding			4	83	16	103
Total	0	0	521	378	55

Variants in DSCAML1

This is a list of pathogenic ClinVar variants found in the DSCAML1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-117428322-CG-C		DSCAML1-related disorder	Benign (May 03, 2019)
11-117428323-G-C		DSCAML1-related disorder	Benign (Oct 17, 2019)
11-117428337-G-C			Likely benign (May 24, 2022)
11-117428345-A-G		not specified	Uncertain significance (Feb 21, 2024)
11-117428350-G-C			Uncertain significance (Dec 12, 2022)
11-117428351-A-G			Uncertain significance (Sep 27, 2023)
11-117428352-G-A			Likely benign (May 12, 2022)
11-117428356-G-A		not specified	Uncertain significance (Jan 29, 2024)
11-117428357-C-A			Uncertain significance (Jul 25, 2022)
11-117428357-C-T			Uncertain significance (Aug 23, 2022)
11-117428361-G-A			Likely benign (Nov 21, 2023)
11-117428362-G-A			Uncertain significance (Dec 11, 2023)
11-117428363-C-T		DSCAML1-related disorder	Likely benign (Jan 25, 2024)
11-117428364-C-T			Likely benign (May 17, 2022)
11-117428387-C-A			Uncertain significance (Nov 03, 2022)
11-117428390-C-T		not specified	Uncertain significance (Jun 23, 2023)
11-117428391-C-T			Likely benign (Nov 01, 2023)
11-117428405-C-T		not specified	Uncertain significance (Jul 25, 2023)
11-117428406-G-A			Benign (Dec 25, 2023)
11-117428412-C-T			Likely benign (Dec 04, 2023)
11-117428427-C-T			Likely benign (Jan 29, 2024)
11-117428428-C-T			Uncertain significance (May 08, 2023)
11-117428430-C-T			Uncertain significance (Jan 07, 2024)
11-117428440-T-C			Uncertain significance (Jan 02, 2023)
11-117428446-C-T			Uncertain significance (May 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DSCAML1	protein_coding	protein_coding	ENST00000321322	33	389752

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.59e-9	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.15	1030	1.36e+3	0.759	0.0000911	13671
Missense in Polyphen		320	546.07	0.586		5256
Synonymous	-2.05	642	579	1.11	0.0000430	4372
Loss of Function	7.88	8	87.6	0.0913	0.00000444	965

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000184
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000892	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell adhesion molecule that plays a role in neuronal self-avoidance (PubMed:11453658). Promotes repulsion between specific neuronal processes of either the same cell or the same subtype of cells. Promotes both isoneuronal self-avoidance for creating an orderly neurite arborization in retinal rod bipolar cells and heteroneuronal self-avoidance to maintain mosaic spacing between AII amacrine cells (By similarity). Adhesion molecule that promotes lamina-specific synaptic connections in the retina: expressed in specific subsets of interneurons and retinal ganglion cells (RGCs) and promotes synaptic connectivity via homophilic interactions (By similarity). {ECO:0000250|UniProtKB:E1C8P7, ECO:0000250|UniProtKB:Q4VA61, ECO:0000269|PubMed:11453658}.
• Pathway: Developmental Biology;DSCAM interactions;Netrin-1 signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.257
• rvis_EVS: -4.22
• rvis_percentile_EVS: 0.15

Haploinsufficiency Scores

• pHI: 0.371
• hipred: Y
• hipred_score: 0.693
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.326

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dscaml1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: cell fate determination;homophilic cell adhesion via plasma membrane adhesion molecules;axonogenesis;axon guidance;central nervous system development;brain development;dorsal/ventral pattern formation;embryonic skeletal system morphogenesis;dendrite self-avoidance
• Cellular component: extracellular space;plasma membrane;cell surface;integral component of membrane;cell junction;axon;synapse
• Molecular function: protein homodimerization activity;cell-cell adhesion mediator activity