SMIM24

small integral membrane protein 24

Basic information

Region (hg38): 19:3473985-3480525

Previous symbols: [ "C19orf77" ]

Links

ENSG00000095932 ∙ NCBI:284422 ∙ ∙ HGNC:37244 ∙ Uniprot:O75264 ∙ 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 SMIM24 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM24 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in SMIM24

This is a list of pathogenic ClinVar variants found in the SMIM24 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-3474853-G-A		not specified	Uncertain significance (Dec 27, 2023)
19-3474868-T-A		not specified	Uncertain significance (Dec 03, 2021)
19-3474878-C-T		not specified	Likely benign (Jun 10, 2022)
19-3474931-G-C		not specified	Uncertain significance (Apr 25, 2022)
19-3474967-T-C		not specified	Uncertain significance (Sep 27, 2021)
19-3474985-C-T		not specified	Uncertain significance (Dec 16, 2023)
19-3478477-C-A		not specified	Uncertain significance (Oct 12, 2022)
19-3478864-C-T		not specified	Uncertain significance (Apr 20, 2024)
19-3478899-A-G		not specified	Uncertain significance (Mar 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM24	protein_coding	protein_coding	ENST00000215531	4	6136

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0747	0.759	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.514	53	64.6	0.820	0.00000330	834
Missense in Polyphen		13	15.601	0.83328		200
Synonymous	0.749	23	28.0	0.820	0.00000163	244
Loss of Function	0.984	2	4.17	0.480	1.79e-7	54

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

Intolerance Scores

• rvis_EVS: 0.83
• rvis_percentile_EVS: 88.16

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Smim24

Gene ontology

• Biological process: biological_process
• Cellular component: integral component of membrane
• Molecular function: molecular_function