SMAP1

small ArfGAP 1, the group of ArfGAPs

Basic information

Region (hg38): 6:70667776-70862011

Links

ENSG00000112305 ∙ NCBI:60682 ∙ OMIM:611372 ∙ HGNC:19651 ∙ Uniprot:Q8IYB5 ∙ 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 SMAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMAP1 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				1		1
missense			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	18	2	1

Variants in SMAP1

This is a list of pathogenic ClinVar variants found in the SMAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-70668103-A-C		not specified	Uncertain significance (Jun 18, 2024)
6-70755016-C-T		not specified	Uncertain significance (May 29, 2024)
6-70755029-A-G		not specified	Uncertain significance (Aug 03, 2021)
6-70773374-T-G		not specified	Uncertain significance (Jun 03, 2024)
6-70773414-G-A		not specified	Uncertain significance (Jul 05, 2023)
6-70791698-T-C		not specified	Uncertain significance (Mar 29, 2024)
6-70798667-A-G		not specified	Uncertain significance (Sep 20, 2023)
6-70798712-C-T		not specified	Uncertain significance (Apr 01, 2024)
6-70836963-T-C		not specified	Uncertain significance (Apr 17, 2024)
6-70836999-C-T			Benign (Jun 24, 2021)
6-70852595-C-T			Likely benign (Feb 01, 2024)
6-70856916-G-T		not specified	Uncertain significance (Jan 23, 2023)
6-70857922-G-A		not specified	Uncertain significance (Jun 04, 2024)
6-70857940-C-G		not specified	Uncertain significance (Jan 25, 2024)
6-70857946-T-C		not specified	Uncertain significance (Dec 27, 2022)
6-70857990-T-C		not specified	Uncertain significance (Jun 01, 2023)
6-70858024-T-C		not specified	Uncertain significance (Dec 15, 2022)
6-70858047-A-G		not specified	Uncertain significance (Aug 12, 2021)
6-70858131-G-A		not specified	Uncertain significance (Mar 06, 2023)
6-70858131-G-C		not specified	Uncertain significance (Apr 11, 2023)
6-70858135-T-C		not specified	Uncertain significance (Aug 12, 2022)
6-70858186-T-C		not specified	Uncertain significance (May 16, 2022)
6-70860200-A-G		not specified	Likely benign (May 01, 2022)
6-70860242-C-A		not specified	Uncertain significance (Aug 10, 2021)
6-70860246-C-T		not specified	Uncertain significance (Apr 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMAP1	protein_coding	protein_coding	ENST00000370455	11	194240

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.994	0.00643	125739	0	6	125745	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	193	241	0.801	0.0000112	3035
Missense in Polyphen		44	80.899	0.54389		1042
Synonymous	-0.457	91	85.6	1.06	0.00000445	905
Loss of Function	4.15	2	23.8	0.0839	0.00000115	281

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000378	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTPase activating protein that acts on ARF6. Plays a role in clathrin-dependent endocytosis. May play a role in erythropoiesis (By similarity). {ECO:0000250}.
• Pathway: Endocytosis - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.521
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.35

Haploinsufficiency Scores

• pHI: 0.252
• hipred: Y
• hipred_score: 0.594
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.380

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smap1
• Phenotype: liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); neoplasm; hematopoietic system phenotype; cellular phenotype; immune system phenotype

Gene ontology

• Biological process: positive regulation of GTPase activity;positive regulation of erythrocyte differentiation;regulation of clathrin-dependent endocytosis
• Cellular component: cytoplasm;plasma membrane
• Molecular function: GTPase activator activity;clathrin binding;metal ion binding