SMIM1

small integral membrane protein 1 (Vel blood group), the group of Blood group antigens

Basic information

Region (hg38): 1:3772749-3775982

Links

ENSG00000235169 ∙ NCBI:388588 ∙ OMIM:615242 ∙ HGNC:44204 ∙ Uniprot:B2RUZ4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Blood group, Vel system	BG	Hematologic	Variants associated with a blood group may be important in specific situations (eg, related to transfusion)	Hematologic	23505126; 23563606; 23563608

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SMIM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM1 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	2	0

Variants in SMIM1

This is a list of pathogenic ClinVar variants found in the SMIM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-3775430-C-T		SMIM1-related disorder	Likely benign (Jul 11, 2019)
1-3775433-AGTCAGCCTAGGGGCTGT-A		Vel blood group system	Affects (May 01, 2013)
1-3775473-C-T		not specified	Likely benign (Jan 30, 2024)
1-3775480-G-A		not specified	Uncertain significance (Aug 28, 2024)
1-3775795-G-T		not specified	Uncertain significance (Jan 08, 2024)
1-3775809-T-G		not specified	Uncertain significance (May 24, 2023)
1-3775818-G-A		not specified	Uncertain significance (Nov 12, 2021)
1-3775884-G-A		not specified	Uncertain significance (May 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM1	protein_coding	protein_coding	ENST00000444870	2	3195

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0330	0.629	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.827	31	46.9	0.660	0.00000273	504
Missense in Polyphen		7	12.772	0.54805		164
Synonymous	0.530	18	21.1	0.853	0.00000145	153
Loss of Function	0.286	2	2.49	0.804	1.06e-7	30

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of red blood cell formation. {ECO:0000250|UniProtKB:B3DHH5}.

Haploinsufficiency Scores

• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Smim1

Zebrafish Information Network

• Gene name: smim1
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Cellular component: plasma membrane;cell surface;integral component of membrane
• Molecular function: protein homodimerization activity