LETMD1

LETM1 domain containing 1, the group of Solute carrier family 55, LETM mitochondrial cation/proton exchangers

Basic information

Region (hg38): 12:51047962-51060424

Links

ENSG00000050426 ∙ NCBI:25875 ∙ OMIM:619070 ∙ HGNC:24241 ∙ Uniprot:Q6P1Q0 ∙ 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 LETMD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LETMD1 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			24	3		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	3	0

Variants in LETMD1

This is a list of pathogenic ClinVar variants found in the LETMD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-51048366-T-A		not specified	Uncertain significance (Jan 30, 2024)
12-51048373-T-C		not specified	Uncertain significance (Aug 12, 2022)
12-51048388-C-T		not specified	Likely benign (May 14, 2024)
12-51049044-C-G		not specified	Uncertain significance (Oct 06, 2022)
12-51049083-T-G		not specified	Uncertain significance (May 27, 2022)
12-51049086-T-C		not specified	Uncertain significance (Nov 28, 2023)
12-51049090-T-C		not specified	Uncertain significance (Jan 08, 2024)
12-51049137-G-C		not specified	Uncertain significance (Jul 09, 2021)
12-51049141-G-A		not specified	Uncertain significance (Sep 06, 2022)
12-51049149-C-T		not specified	Uncertain significance (Nov 12, 2021)
12-51049164-C-A		not specified	Uncertain significance (Dec 13, 2022)
12-51053802-C-T		not specified	Uncertain significance (Nov 10, 2022)
12-51055844-T-A		not specified	Uncertain significance (Jan 06, 2023)
12-51055909-A-G		not specified	Uncertain significance (Jul 14, 2021)
12-51055915-C-G		not specified	Uncertain significance (Nov 27, 2023)
12-51055920-C-T		not specified	Uncertain significance (Jan 16, 2024)
12-51055962-G-T		not specified	Uncertain significance (Feb 10, 2022)
12-51055969-C-T		not specified	Uncertain significance (May 20, 2024)
12-51055995-T-C		not specified	Uncertain significance (Oct 12, 2021)
12-51055998-C-T		not specified	Uncertain significance (Sep 13, 2023)
12-51055999-G-A		not specified	Likely benign (Aug 16, 2021)
12-51056151-G-A		not specified	Likely benign (Aug 22, 2022)
12-51056154-G-T		not specified	Uncertain significance (Apr 07, 2023)
12-51056165-G-A		not specified	Uncertain significance (Aug 11, 2022)
12-51056243-G-A		not specified	Likely benign (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LETMD1	protein_coding	protein_coding	ENST00000418425	9	12463

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0485	0.951	125717	0	30	125747	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.543	193	215	0.896	0.0000119	2408
Missense in Polyphen		41	53.426	0.76742		608
Synonymous	-1.07	89	77.0	1.16	0.00000381	752
Loss of Function	2.91	6	20.1	0.299	9.19e-7	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000472	0.000472
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000979	0.0000967
Middle Eastern	0.000163	0.000163
South Asian	0.0000991	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in tumorigenesis and may function as a negative regulator of the p53/TP53. {ECO:0000269|PubMed:12879013}.

Recessive Scores

• pRec: 0.0774

Intolerance Scores

• loftool: 0.568
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.0979
• hipred: N
• hipred_score: 0.423
• ghis: 0.513

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.907

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Letmd1

Gene ontology

• Cellular component: nucleoplasm;mitochondrion;mitochondrial outer membrane;mitochondrial inner membrane;integral component of membrane
• Molecular function: protein binding;ribosome binding