SMIM12

small integral membrane protein 12

Basic information

Region (hg38): 1:34712736-34859755

Previous symbols: [ "C1orf212" ]

Links

ENSG00000163866 ∙ NCBI:113444 ∙ ∙ HGNC:25154 ∙ Uniprot:Q96EX1 ∙ 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 SMIM12 gene.

• not provided (181 variants)
• Erythrokeratodermia variabilis et progressiva 1 (75 variants)
• Inborn genetic diseases (61 variants)
• not specified (30 variants)
• Erythrokeratodermia variabilis et progressiva 2 (8 variants)
• Autosomal dominant nonsyndromic hearing loss 2B (4 variants)
• Nonsyndromic Hearing Loss, Dominant (3 variants)
• GJB3-related condition (2 variants)
• Autosomal recessive nonsyndromic hearing loss 1A;Autosomal dominant nonsyndromic hearing loss 2B;Erythrokeratodermia variabilis et progressiva 1 (2 variants)
• Autosomal dominant nonsyndromic hearing loss 2B;Erythrokeratodermia variabilis et progressiva 1;Autosomal recessive nonsyndromic hearing loss 1A (1 variants)
• Autosomal recessive nonsyndromic hearing loss 1A;Autosomal dominant nonsyndromic hearing loss 3A (1 variants)
• Deafness, autosomal dominant, with peripheral neuropathy (1 variants)
• Erythrokeratodermia variabilis et progressiva 1;Autosomal dominant nonsyndromic hearing loss 2B;Autosomal recessive nonsyndromic hearing loss 1A (1 variants)
• Hearing impairment (1 variants)
• Autosomal dominant nonsyndromic hearing loss 2B;Autosomal recessive nonsyndromic hearing loss 1A;Erythrokeratodermia variabilis et progressiva 1 (1 variants)
• Nonsyndromic Deafness (1 variants)
• Autosomal recessive nonsyndromic hearing loss 1A (1 variants)
• Deafness, digenic, GJB2/GJB3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMIM12 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	2	5	163	44	43	257
Total	2	5	164	44	43

Highest pathogenic variant AF is 0.0000854

Variants in SMIM12

This is a list of pathogenic ClinVar variants found in the SMIM12 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-34757356-T-C		not specified	Uncertain significance (Jul 06, 2021)
1-34757394-C-T		not specified	Uncertain significance (Aug 30, 2021)
1-34757413-T-C		not specified	Uncertain significance (Dec 14, 2023)
1-34757418-A-G		not specified	Uncertain significance (Apr 04, 2023)
1-34757455-G-A		not specified	Uncertain significance (Apr 07, 2022)
1-34757529-G-A		not specified	Uncertain significance (Nov 30, 2021)
1-34757554-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-34757622-C-T		not specified	Uncertain significance (Jan 18, 2022)
1-34757640-A-G		not specified	Uncertain significance (Jun 29, 2023)
1-34757692-G-T		not specified	Uncertain significance (Feb 15, 2023)
1-34757695-A-G		not specified	Uncertain significance (Feb 22, 2023)
1-34757750-C-A		not specified	Uncertain significance (Jun 10, 2022)
1-34757751-G-A		not specified	Uncertain significance (Jul 29, 2022)
1-34757821-G-A		not specified	Uncertain significance (Jun 23, 2023)
1-34757842-A-G		not specified	Uncertain significance (Apr 25, 2022)
1-34757878-A-G		not specified	Uncertain significance (Jul 26, 2022)
1-34757916-A-G		not specified	Likely benign (Feb 05, 2024)
1-34758097-A-G		not specified	Uncertain significance (Feb 15, 2023)
1-34758117-C-T		not specified	Uncertain significance (Apr 20, 2023)
1-34758118-G-A		not specified	Likely benign (Aug 23, 2021)
1-34760655-T-C			Benign (Nov 12, 2018)
1-34761254-CA-C		Erythrokeratodermia variabilis et progressiva 2	Uncertain significance (Mar 25, 2024)
1-34761261-T-C		Inborn genetic diseases	Uncertain significance (Aug 04, 2023)
1-34761289-G-A		Erythrokeratodermia variabilis et progressiva 2	Pathogenic (Apr 01, 2003)
1-34761291-G-A			Likely benign (Dec 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMIM12	protein_coding	protein_coding	ENST00000521580	1	147080

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.567	0.390	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	32	57.7	0.554	0.00000367	586
Missense in Polyphen		8	18.258	0.43816		174
Synonymous	0.574	20	23.5	0.850	0.00000146	185
Loss of Function	1.48	0	2.55	0.00	1.09e-7	31

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: 0.15
• rvis_percentile_EVS: 63.81

Haploinsufficiency Scores

• pHI: 0.0590
• hipred: N
• hipred_score: 0.384
• ghis: 0.537

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: Smim12

Gene ontology

• Cellular component: integral component of membrane