SMIM17

small integral membrane protein 17

Basic information

Region (hg38): 19:56643159-56657247

Links

ENSG00000268182 ∙ NCBI:147670 ∙ ∙ HGNC:27114 ∙ Uniprot:P0DL12 ∙ 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 SMIM17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM17 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in SMIM17

This is a list of pathogenic ClinVar variants found in the SMIM17 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-56645696-G-A		not specified	Uncertain significance (Oct 29, 2024)
19-56645717-G-A		not specified	Uncertain significance (Jan 07, 2025)
19-56645717-G-C		not specified	Uncertain significance (Mar 01, 2025)
19-56645720-C-T		not specified	Uncertain significance (Jul 13, 2022)
19-56645724-G-C		not specified	Uncertain significance (Apr 01, 2024)
19-56645735-C-T		not specified	Uncertain significance (Mar 07, 2023)
19-56645738-G-A		not specified	Likely benign (Sep 01, 2021)
19-56645747-G-A		not specified	Uncertain significance (Jul 06, 2021)
19-56645747-G-T		not specified	Uncertain significance (Feb 08, 2025)
19-56645770-C-T		not specified	Uncertain significance (Jan 04, 2024)
19-56645803-G-C		not specified	Uncertain significance (Mar 01, 2023)
19-56647600-C-T		not specified	Uncertain significance (Feb 01, 2025)
19-56647630-C-A		not specified	Uncertain significance (Jan 21, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM17	protein_coding	protein_coding	ENST00000598409	3	12622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0147	0.701	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.368	49	56.8	0.863	0.00000310	762
Missense in Polyphen		12	17.741	0.67641		273
Synonymous	0.314	20	21.9	0.915	0.00000124	229
Loss of Function	0.636	3	4.45	0.674	1.91e-7	57

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

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smim17

Gene ontology

• Cellular component: integral component of membrane