SMDT1

single-pass membrane protein with aspartate rich tail 1

Basic information

Region (hg38): 22:42079691-42084284

Previous symbols: [ "C22orf32" ]

Links

ENSG00000183172 ∙ NCBI:91689 ∙ OMIM:615588 ∙ HGNC:25055 ∙ Uniprot:Q9H4I9 ∙ 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 SMDT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMDT1 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in SMDT1

This is a list of pathogenic ClinVar variants found in the SMDT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-42079785-C-T		not specified	Uncertain significance (Jul 14, 2023)
22-42079806-C-T		not specified	Uncertain significance (Oct 27, 2021)
22-42079820-G-C		not specified	Uncertain significance (Feb 13, 2023)
22-42079820-G-T		not specified	Uncertain significance (Dec 20, 2023)
22-42079835-C-T		not specified	Uncertain significance (Oct 05, 2023)
22-42079838-A-G		not specified	Uncertain significance (Dec 27, 2023)
22-42079873-G-T		not specified	Uncertain significance (Sep 07, 2022)
22-42079880-T-C		not specified	Uncertain significance (Oct 26, 2022)
22-42079899-C-G		not specified	Uncertain significance (Apr 01, 2024)
22-42079913-A-C		not specified	Uncertain significance (Dec 20, 2023)
22-42081937-C-A		not specified	Uncertain significance (Nov 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMDT1	protein_coding	protein_coding	ENST00000331479	2	4594

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.183	0.658	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.101	69	66.7	1.03	0.00000328	683
Missense in Polyphen		28	28.293	0.98965		295
Synonymous	-1.78	42	29.7	1.42	0.00000146	240
Loss of Function	0.894	1	2.54	0.394	1.06e-7	34

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000210
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	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential regulatory subunit of the mitochondrial calcium uniporter complex (uniplex), a complex that mediates calcium uptake into mitochondria (PubMed:24231807, PubMed:26774479, PubMed:27099988). Required to bridge the calcium- sensing proteins MICU1 and MICU2 with the calcium-conducting subunit MCU (PubMed:24231807). Plays a central role in regulating the uniplex complex response to intracellular calcium signaling (PubMed:27099988). Acts by mediating activation of MCU and retention of MICU1 to the MCU pore, in order to ensure tight regulation of the uniplex complex and appropriate responses to intracellular calcium signaling (PubMed:27099988). {ECO:0000269|PubMed:24231807, ECO:0000269|PubMed:26774479, ECO:0000269|PubMed:27099988}.
• Pathway: Transport of small molecules;Mitochondrial calcium ion transport;Processing of SMDT1 (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: -0.27
• rvis_percentile_EVS: 33.97

Haploinsufficiency Scores

• pHI: 0.172
• hipred: N
• hipred_score: 0.198
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• 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: Smdt1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: mitochondrial calcium ion transmembrane transport;calcium import into the mitochondrion;mitochondrial calcium ion homeostasis
• Cellular component: nucleus;mitochondrion;mitochondrial inner membrane;mitochondrial matrix;integral component of mitochondrial inner membrane;uniplex complex
• Molecular function: protein binding