MMS22L

MMS22 like, DNA repair protein

Basic information

Region (hg38): 6:97142161-97283217

Previous symbols: [ "C6orf167" ]

Links

ENSG00000146263 ∙ NCBI:253714 ∙ OMIM:615614 ∙ HGNC:21475 ∙ Uniprot:Q6ZRQ5 ∙ 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 MMS22L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MMS22L 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				1		1
missense			54	3		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	4	0

Variants in MMS22L

This is a list of pathogenic ClinVar variants found in the MMS22L region.

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

Position	Type	Phenotype	Significance	ClinVar
6-97146879-T-C		not specified	Uncertain significance (Mar 02, 2023)
6-97149904-G-C		not specified	Uncertain significance (Jun 19, 2024)
6-97149920-A-T		not specified	Uncertain significance (Jan 02, 2024)
6-97149985-T-C		not specified	Uncertain significance (Dec 09, 2023)
6-97150000-C-T		not specified	Uncertain significance (Nov 08, 2022)
6-97150016-A-T		not specified	Uncertain significance (Feb 05, 2024)
6-97151814-C-G		not specified	Uncertain significance (Dec 17, 2023)
6-97162106-G-T		not specified	Uncertain significance (Jun 28, 2023)
6-97165262-T-C		not specified	Likely benign (Apr 07, 2022)
6-97165378-T-C		not specified	Uncertain significance (Jan 23, 2024)
6-97165394-T-C		not specified	Uncertain significance (Jun 01, 2023)
6-97165445-C-T		not specified	Uncertain significance (Mar 01, 2023)
6-97165451-A-G		not specified	Uncertain significance (Jul 19, 2022)
6-97168151-G-A		not specified	Uncertain significance (Oct 25, 2022)
6-97173064-C-T		not specified	Uncertain significance (Aug 15, 2023)
6-97173095-C-T		not specified	Uncertain significance (Nov 17, 2022)
6-97173171-T-C		not specified	Uncertain significance (Jun 21, 2021)
6-97173174-C-G		not specified	Uncertain significance (Jun 06, 2023)
6-97173198-C-T		not specified	Uncertain significance (Nov 05, 2021)
6-97173199-G-A		not specified	Likely benign (Dec 27, 2023)
6-97178484-T-C		not specified	Uncertain significance (Dec 14, 2021)
6-97178519-C-T		not specified	Likely benign (Aug 30, 2021)
6-97179533-G-A		not specified	Uncertain significance (Apr 18, 2023)
6-97181958-T-C		not specified	Uncertain significance (May 22, 2023)
6-97181983-T-C		not specified	Uncertain significance (Oct 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MMS22L	protein_coding	protein_coding	ENST00000275053	24	141057

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000830	1.00	125675	0	73	125748	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.293	585	605	0.966	0.0000279	8099
Missense in Polyphen		242	272.71	0.88738		3748
Synonymous	-0.161	229	226	1.01	0.0000107	2320
Loss of Function	5.36	21	69.0	0.304	0.00000342	870

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000528	0.000514
Ashkenazi Jewish	0.00149	0.00149
East Asian	0.000503	0.000489
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000217	0.000211
Middle Eastern	0.000503	0.000489
South Asian	0.000164	0.000163
Other	0.000823	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the MMS22L-TONSL complex, a complex that stimulates the recombination-dependent repair of stalled or collapsed replication forks. The MMS22L-TONSL complex is required to maintain genome integrity during DNA replication by promoting homologous recombination-mediated repair of replication fork- associated double-strand breaks. It may act by mediating the assembly of RAD51 filaments on ssDNA. {ECO:0000269|PubMed:21055983, ECO:0000269|PubMed:21055984, ECO:0000269|PubMed:21055985}.

Intolerance Scores

• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.83

Haploinsufficiency Scores

• pHI: 0.113
• hipred: Y
• hipred_score: 0.698
• ghis: 0.556

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mms22l
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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: double-strand break repair via homologous recombination;replication fork processing
• Cellular component: nucleoplasm;cytosol;FACT complex;MCM complex;nuclear replication fork
• Molecular function: protein binding