SMIM7

small integral membrane protein 7

Basic information

Region (hg38): 19:16630751-16660442

Previous symbols: [ "C19orf42" ]

Links

ENSG00000214046 ∙ NCBI:79086 ∙ ∙ HGNC:28419 ∙ Uniprot:Q9BQ49 ∙ 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 SMIM7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM7 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						0
Total	0	0	7	0	0

Variants in SMIM7

This is a list of pathogenic ClinVar variants found in the SMIM7 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-16654036-C-G		not specified	Uncertain significance (Apr 23, 2024)
19-16654042-T-C		not specified	Uncertain significance (Aug 26, 2024)
19-16654090-A-G		not specified	Uncertain significance (Dec 03, 2024)
19-16654125-C-T		not specified	Uncertain significance (Aug 23, 2021)
19-16659440-T-C		not specified	Uncertain significance (Nov 12, 2021)
19-16659981-C-G		not specified	Uncertain significance (Feb 15, 2023)
19-16659984-C-T		not specified	Uncertain significance (Oct 02, 2023)
19-16659986-T-C		not specified	Uncertain significance (Mar 01, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM7	protein_coding	protein_coding	ENST00000487416	5	29692

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00485	0.706	124785	0	5	124790	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.418	52	44.2	1.18	0.00000239	499
Missense in Polyphen		18	15.536	1.1586		152
Synonymous	-1.27	24	17.3	1.39	9.45e-7	126
Loss of Function	0.715	4	5.87	0.682	3.15e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000581	0.0000581
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.224
• hipred: N
• hipred_score: 0.132
• ghis: 0.653

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smim7

Gene ontology

• Cellular component: integral component of membrane