SMAP2

small ArfGAP2, the group of ArfGAPs

Basic information

Region (hg38): 1:40344849-40423326

Previous symbols: [ "SMAP1L" ]

Links

ENSG00000084070

∙ NCBI:64744 ∙ OMIM:616916 ∙ HGNC:25082 ∙ Uniprot:Q8WU79 ∙ 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 SMAP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMAP2 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			1 clinvar			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in SMAP2

This is a list of pathogenic ClinVar variants found in the SMAP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-40417055-G-A		not specified	Uncertain significance (Sep 01, 2021)	2351543

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMAP2	protein_coding	protein_coding	ENST00000372718	10	78477

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0178	0.982	125537	0	207	125744	0.000823

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	180	247	0.728	0.0000123	2841
Missense in Polyphen		39	71.914	0.54232		883
Synonymous	1.28	71	86.1	0.825	0.00000469	812
Loss of Function	3.28	8	26.1	0.307	0.00000160	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000764	0.000763
Ashkenazi Jewish	0.0115	0.0116
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000423	0.000422
Middle Eastern	0.00	0.00
South Asian	0.000327	0.000327
Other	0.00147	0.00147

dbNSFP

Source: dbNSFP

Function: FUNCTION: GTPase activating protein that acts on ARF1. Can also activate ARF6 (in vitro). May play a role in clathrin-dependent retrograde transport from early endosomes to the trans-Golgi network (By similarity). {ECO:0000250}.;
Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Recessive Scores

pRec: 0.107

Intolerance Scores

loftool: 0.620
rvis_EVS: -0.29
rvis_percentile_EVS: 32.94

Haploinsufficiency Scores

pHI: 0.354
hipred: Y
hipred_score: 0.554
ghis: 0.586

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.356

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Smap2
Phenotype: cellular phenotype; reproductive system phenotype;

Gene ontology

Biological process: positive regulation of GTPase activity
Cellular component: cytoplasm
Molecular function: GTPase activator activity;protein binding;metal ion binding