NSMCE4A

NSE4 homolog A, SMC5-SMC6 complex component, the group of SMC5-6 protein complex

Basic information

Region (hg38): 10:121957091-121975217

Previous symbols: [ "C10orf86" ]

Links

ENSG00000107672 ∙ NCBI:54780 ∙ OMIM:612987 ∙ HGNC:25935 ∙ Uniprot:Q9NXX6 ∙ 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 NSMCE4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSMCE4A 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	27	0	0

Variants in NSMCE4A

This is a list of pathogenic ClinVar variants found in the NSMCE4A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-121959389-T-C		not specified	Uncertain significance (Feb 21, 2025)
10-121959556-T-C		not specified	Uncertain significance (Dec 09, 2023)
10-121960372-C-T		not specified	Uncertain significance (Jun 01, 2023)
10-121960414-G-A			Likely benign (Nov 01, 2022)
10-121961428-T-A		not specified	Uncertain significance (Oct 03, 2022)
10-121961461-T-G		not specified	Uncertain significance (Dec 19, 2022)
10-121961464-G-A		not specified	Uncertain significance (Jun 05, 2023)
10-121961511-G-A		not specified	Uncertain significance (Feb 10, 2023)
10-121961514-T-A		not specified	Uncertain significance (Sep 20, 2023)
10-121965311-T-C		not specified	Uncertain significance (Dec 31, 2024)
10-121965375-T-C		not specified	Uncertain significance (Jun 18, 2024)
10-121967662-G-A		not specified	Uncertain significance (Oct 21, 2024)
10-121967671-G-A		not specified	Uncertain significance (Oct 01, 2024)
10-121967769-T-G		not specified	Uncertain significance (Dec 03, 2024)
10-121967784-G-A		not specified	Uncertain significance (May 15, 2024)
10-121967791-C-T		not specified	Uncertain significance (Jun 21, 2023)
10-121967793-C-T		not specified	Uncertain significance (Feb 06, 2025)
10-121967796-A-G		not specified	Uncertain significance (Jul 16, 2024)
10-121967806-G-A		not specified	Uncertain significance (Feb 05, 2025)
10-121970970-G-T		not specified	Uncertain significance (May 24, 2023)
10-121970976-A-G		not specified	Uncertain significance (Nov 10, 2024)
10-121974075-C-A		not specified	Uncertain significance (Sep 25, 2023)
10-121974960-T-G		not specified	Uncertain significance (Dec 21, 2022)
10-121974963-A-G		not specified	Uncertain significance (Jun 17, 2024)
10-121974972-T-C		not specified	Uncertain significance (Nov 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NSMCE4A	protein_coding	protein_coding	ENST00000369023	10	18130

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0145	0.984	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	135	185	0.730	0.00000966	2501
Missense in Polyphen		47	74.41	0.63163		973
Synonymous	1.07	51	61.7	0.826	0.00000298	729
Loss of Function	2.85	7	21.1	0.331	0.00000132	238

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000166	0.000163
Finnish	0.000508	0.000508
European (Non-Finnish)	0.0000926	0.0000879
Middle Eastern	0.000166	0.000163
South Asian	0.000137	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the SMC5-SMC6 complex, a complex involved in DNA double-strand breaks by homologous recombination. The complex may promote sister chromatid homologous recombination by recruiting the SMC1-SMC3 cohesin complex to double-strand breaks. The complex is required for telomere maintenance via recombination in ALT (alternative lengthening of telomeres) cell lines and mediates sumoylation of shelterin complex (telosome) components which is proposed to lead to shelterin complex disassembly in ALT- associated PML bodies (APBs). Is involved in positive regulation of response to DNA damage stimulus. {ECO:0000269|PubMed:18086888}.
• Pathway: SUMOylation of DNA damage response and repair proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;SUMOylation (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.626
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.449
• hipred: Y
• hipred_score: 0.550
• ghis: 0.627

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0959

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nsmce4a

Gene ontology

• Biological process: DNA repair;DNA recombination;positive regulation of response to DNA damage stimulus
• Cellular component: chromosome, telomeric region;nucleus;nucleoplasm;nuclear body;Smc5-Smc6 complex
• Molecular function: protein binding