SAMM50

SAMM50 sorting and assembly machinery component, the group of Mitochondrial sorting and assembly machinery complex

Basic information

Region (hg38): 22:43955441-44010531

Links

ENSG00000100347 ∙ NCBI:25813 ∙ OMIM:612058 ∙ HGNC:24276 ∙ Uniprot:Q9Y512 ∙ 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 SAMM50 gene.

• Inborn genetic diseases (17 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMM50 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					5	5
missense			17	1		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	17	1	6

Variants in SAMM50

This is a list of pathogenic ClinVar variants found in the SAMM50 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-43955596-C-T		not specified	Uncertain significance (Sep 22, 2023)
22-43963301-C-G		not specified	Uncertain significance (Jun 12, 2023)
22-43963335-A-G		not specified	Uncertain significance (Nov 13, 2023)
22-43963366-A-G			Benign (Jul 13, 2018)
22-43963368-C-T		not specified	Uncertain significance (Jan 27, 2022)
22-43963386-A-C		not specified	Uncertain significance (May 27, 2022)
22-43964455-G-A			Likely benign (May 08, 2018)
22-43968737-C-T		not specified	Uncertain significance (Mar 07, 2024)
22-43972253-A-G		not specified	Uncertain significance (Oct 29, 2021)
22-43972265-G-A		not specified	Uncertain significance (Oct 10, 2023)
22-43972316-A-G		not specified	Uncertain significance (Jul 06, 2021)
22-43972324-A-G			Benign (Mar 26, 2021)
22-43972861-C-T			Benign (Dec 31, 2019)
22-43972905-G-A		not specified	Uncertain significance (Jan 10, 2022)
22-43972979-C-T		not specified	Uncertain significance (Sep 22, 2022)
22-43972985-G-A		not specified	Uncertain significance (Mar 02, 2023)
22-43973257-A-T		not specified	Uncertain significance (Jul 09, 2021)
22-43973288-C-T		not specified	Uncertain significance (May 03, 2023)
22-43973289-G-A		not specified	Uncertain significance (Jun 29, 2023)
22-43973296-G-A			Benign (Nov 20, 2018)
22-43976064-T-G		not specified	Uncertain significance (Oct 27, 2021)
22-43976070-A-G		not specified	Uncertain significance (Jan 16, 2024)
22-43976182-C-T		not specified	Uncertain significance (Dec 13, 2023)
22-43976189-G-A			Benign (Aug 05, 2020)
22-43977875-C-A		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMM50	protein_coding	protein_coding	ENST00000350028	15	55111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.88e-9	0.953	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.915	238	281	0.846	0.0000170	3036
Missense in Polyphen		55	85.039	0.64676		817
Synonymous	1.21	89	105	0.850	0.00000680	905
Loss of Function	2.01	18	29.9	0.602	0.00000150	352

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000659	0.000659
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.000172	0.000163
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a crucial role in the maintenance of the structure of mitochondrial cristae and the proper assembly of the mitochondrial respiratory chain complexes (PubMed:22252321, PubMed:25781180). Required for the assembly of TOMM40 into the TOM complex (PubMed:15644312). {ECO:0000269|PubMed:15644312, ECO:0000269|PubMed:22252321, ECO:0000269|PubMed:25781180}.
• Pathway: Metabolism of proteins;Mitochondrial protein import (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.709
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.82

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.414
• ghis: 0.620

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.694

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Samm50

Gene ontology

• Biological process: mitochondrial respiratory chain complex assembly;cristae formation;protein insertion into mitochondrial outer membrane
• Cellular component: mitochondrial sorting and assembly machinery complex;mitochondrion;mitochondrial outer membrane;integral component of membrane;extracellular exosome
• Molecular function: protein binding