SMIM19

small integral membrane protein 19

Basic information

Region (hg38): 8:42541155-42555195

Previous symbols: [ "C8orf40" ]

Links

ENSG00000176209 ∙ NCBI:114926 ∙ ∙ HGNC:25166 ∙ Uniprot:Q96E16 ∙ 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 SMIM19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM19 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			14		3	17
Total	0	0	27	0	3

Variants in SMIM19

This is a list of pathogenic ClinVar variants found in the SMIM19 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-42541812-G-GC		Idiopathic basal ganglia calcification 1	Uncertain significance (Jun 14, 2016)
8-42541815-G-GC		Idiopathic basal ganglia calcification 1	Uncertain significance (Jun 14, 2016)
8-42541835-G-A		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42541844-C-G		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42541861-C-T		Idiopathic basal ganglia calcification 1	Benign (Jan 13, 2018)
8-42541906-A-C		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 12, 2018)
8-42541922-A-C		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 15, 2018)
8-42541928-A-G		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 12, 2018)
8-42541945-C-T		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 12, 2018)
8-42541966-G-A		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 12, 2018)
8-42541967-G-A		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42541971-C-T		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42541992-G-A		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42542013-C-A		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 12, 2018)
8-42542090-T-A		Idiopathic basal ganglia calcification 1	Benign (Jan 13, 2018)
8-42542124-G-T		Idiopathic basal ganglia calcification 1	Uncertain significance (Jan 13, 2018)
8-42542148-G-A		Idiopathic basal ganglia calcification 1	Benign (Jan 13, 2018)
8-42546491-G-C		not specified	Uncertain significance (Mar 07, 2024)
8-42546510-C-T		not specified	Uncertain significance (Mar 02, 2023)
8-42546527-C-G		not specified	Uncertain significance (Mar 29, 2023)
8-42546528-A-G		not specified	Uncertain significance (Aug 10, 2024)
8-42546539-A-T		not specified	Uncertain significance (May 30, 2024)
8-42546549-C-T		not specified	Uncertain significance (Sep 27, 2021)
8-42546593-A-C		not specified	Uncertain significance (Jun 28, 2022)
8-42546593-A-G		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM19	protein_coding	protein_coding	ENST00000438528	3	13306

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.344	0.604	125728	0	3	125731	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.106	58	60.3	0.962	0.00000310	706
Missense in Polyphen		12	16.331	0.73481		233
Synonymous	0.295	20	21.8	0.919	0.00000136	185
Loss of Function	1.52	1	4.46	0.224	1.86e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000910	0.0000909
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.124

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.277
• hipred: N
• hipred_score: 0.328
• ghis: 0.608

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	Medium	Low	Medium
Cancer	Low	Low	Low

Mouse Genome Informatics

• Gene name: Smim19

Gene ontology

• Cellular component: integral component of membrane