SMAGP

small cell adhesion glycoprotein

Basic information

Region (hg38): 12:51244558-51270415

Links

ENSG00000170545 ∙ NCBI:57228 ∙ ∙ HGNC:26918 ∙ Uniprot:Q0VAQ4 ∙ 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 SMAGP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMAGP 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						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in SMAGP

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

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

Position	Type	Phenotype	Significance	ClinVar
12-51245976-C-A		not specified	Uncertain significance (Dec 20, 2023)
12-51245986-C-G		not specified	Uncertain significance (Dec 21, 2022)
12-51246017-T-G		not specified	Uncertain significance (Jul 11, 2023)
12-51246086-G-A		not specified	Uncertain significance (May 13, 2024)
12-51246760-G-C		not specified	Uncertain significance (Jul 06, 2021)
12-51269253-G-A		not specified	Uncertain significance (Aug 13, 2021)
12-51269266-G-C		not specified	Uncertain significance (Feb 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMAGP	protein_coding	protein_coding	ENST00000603798	3	26333

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.254	0.649	124636	0	2	124638	0.00000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0280	51	50.4	1.01	0.00000266	619
Missense in Polyphen		15	18.656	0.80403		248
Synonymous	0.697	18	22.2	0.812	0.00000145	193
Loss of Function	1.22	1	3.46	0.289	1.45e-7	48

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in epithelial cell-cell contacts. May play a role in tumor invasiveness and metastasis formation. {ECO:0000269|PubMed:15986429}.
• Pathway: Integrated Lung Cancer Pathway (Consensus)

Intolerance Scores

• loftool: 0.774
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.170
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smagp

Gene ontology

• Cellular component: nucleoplasm;plasma membrane;integral component of membrane;cell junction;cytoplasmic vesicle membrane
• Molecular function: protein binding