SMIM13

small integral membrane protein 13

Basic information

Region (hg38): 6:11093834-11138733

Previous symbols: [ "C6orf228" ]

Links

ENSG00000224531 ∙ NCBI:221710 ∙ ∙ HGNC:27356 ∙ Uniprot:P0DJ93 ∙ 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 SMIM13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM13 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			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			24			24
Total	0	0	31	0	0

Variants in SMIM13

This is a list of pathogenic ClinVar variants found in the SMIM13 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-11103848-C-A		not specified	Uncertain significance (May 01, 2022)
6-11104505-A-G		not specified	Uncertain significance (Apr 13, 2022)
6-11104526-A-G		not specified	Uncertain significance (Feb 14, 2023)
6-11104541-A-G		not specified	Uncertain significance (Oct 26, 2021)
6-11104551-C-T		not specified	Likely benign (Dec 25, 2024)
6-11104610-C-T		not specified	Uncertain significance (Aug 23, 2021)
6-11104637-G-A		not specified	Uncertain significance (Jan 10, 2023)
6-11104682-G-C		not specified	Uncertain significance (Aug 13, 2021)
6-11104691-A-G		not specified	Uncertain significance (Apr 24, 2024)
6-11104715-G-A		not specified	Uncertain significance (Jun 07, 2024)
6-11104740-G-A		not specified	Uncertain significance (Dec 15, 2023)
6-11104757-A-C		not specified	Uncertain significance (Aug 02, 2021)
6-11104788-G-A		not specified	Uncertain significance (Oct 27, 2021)
6-11104812-G-A		not specified	Uncertain significance (Jan 22, 2025)
6-11104910-C-A		not specified	Uncertain significance (Dec 04, 2024)
6-11104928-A-T		not specified	Uncertain significance (Nov 13, 2024)
6-11104937-A-G		not specified	Uncertain significance (Jun 07, 2023)
6-11104961-A-G		not specified	Uncertain significance (Nov 13, 2024)
6-11104964-T-C		not specified	Uncertain significance (Jul 14, 2021)
6-11105001-G-A		not specified	Uncertain significance (Oct 14, 2023)
6-11105076-C-A		not specified	Uncertain significance (Oct 06, 2024)
6-11105079-A-C		not specified	Uncertain significance (Apr 25, 2022)
6-11105102-G-A		not specified	Uncertain significance (Jan 08, 2024)
6-11105129-G-A		not specified	Uncertain significance (Aug 22, 2023)
6-11105258-C-T		not specified	Uncertain significance (Aug 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM13	protein_coding	protein_coding	ENST00000416247	2	44699

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.192	0.659	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.691	31	43.9	0.706	0.00000228	573
Missense in Polyphen		7	16.692	0.41935		196
Synonymous	-0.204	19	17.9	1.06	8.65e-7	195
Loss of Function	0.944	1	2.66	0.376	1.14e-7	32

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: 0.12
• rvis_percentile_EVS: 62.38

Haploinsufficiency Scores

• ghis: 0.668

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• 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: Smim13

Gene ontology

• Cellular component: integral component of membrane