MNDA

myeloid cell nuclear differentiation antigen, the group of Pyrin domain containing|Pyrin and HIN domain family

Basic information

Region (hg38): 1:158831351-158849506

Links

ENSG00000163563 ∙ NCBI:4332 ∙ OMIM:159553 ∙ HGNC:7183 ∙ Uniprot:P41218 ∙ 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 MNDA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MNDA 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				168		168
missense			343	32		375
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	343	201	0

Variants in MNDA

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

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

Position	Type	Phenotype	Significance	ClinVar
1-158842158-T-C		not specified	Likely benign (Nov 22, 2021)
1-158842159-G-A		not specified	Likely benign (Feb 13, 2022)
1-158842162-T-A		not specified	Uncertain significance (May 12, 2022)
1-158842162-T-C		not specified	Likely benign (Feb 12, 2022)
1-158842162-T-G		not specified	Uncertain significance (Jul 17, 2022)
1-158842165-A-G		not specified	Likely benign (Jun 02, 2022)
1-158842166-T-C		not specified	Uncertain significance (Jul 27, 2023)
1-158842171-G-A		not specified	Likely benign (May 17, 2022)
1-158842175-A-G		not specified	Uncertain significance (Mar 15, 2024)
1-158842177-T-A		not specified	Likely benign (Apr 07, 2022)
1-158842178-C-G		not specified	Likely benign (May 24, 2022)
1-158842181-T-C		not specified	Likely benign (Mar 19, 2022)
1-158842182-T-C		not specified	Uncertain significance (Dec 18, 2022)
1-158842182-T-G		not specified	Uncertain significance (Feb 25, 2024)
1-158842183-G-T		not specified	Uncertain significance (Jul 11, 2022)
1-158842186-G-A		not specified	Likely benign (Dec 05, 2022)
1-158842192-A-G		not specified	Likely benign (Oct 17, 2021)
1-158842192-A-T		not specified	Likely benign (Apr 11, 2024)
1-158842194-T-A		not specified	Uncertain significance (Jan 15, 2022)
1-158842205-G-T		not specified	Uncertain significance (Jan 28, 2024)
1-158842207-T-A		not specified	Uncertain significance (Dec 04, 2023)
1-158842207-T-C		not specified	Likely benign (Jun 01, 2019)
1-158842208-G-A		not specified	Uncertain significance (Sep 30, 2022)
1-158842211-T-C		not specified	Uncertain significance (Dec 08, 2023)
1-158842226-A-G		not specified	Uncertain significance (Nov 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MNDA	protein_coding	protein_coding	ENST00000368141	6	18190

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.09e-17	0.000677	125668	0	6	125674	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.994	248	208	1.19	0.0000102	2670
Missense in Polyphen		69	50.614	1.3633		720
Synonymous	-1.87	100	78.8	1.27	0.00000427	761
Loss of Function	-1.27	22	16.4	1.34	8.20e-7	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000165	0.000158
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000570	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.0000570	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a transcriptional activator/repressor in the myeloid lineage. Plays a role in the granulocyte/monocyte cell- specific response to interferon. Stimulates the DNA binding of the transcriptional repressor protein YY1.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0979

Intolerance Scores

• loftool: 0.963
• rvis_EVS: 0.2
• rvis_percentile_EVS: 67.3

Haploinsufficiency Scores

• pHI: 0.0732
• hipred: N
• hipred_score: 0.112
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.234

Gene Damage Prediction

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

Gene ontology

• Biological process: activation of innate immune response;cellular defense response;cellular response to DNA damage stimulus;negative regulation of B cell proliferation;cellular response to interferon-beta;positive regulation of apoptotic process;neutrophil degranulation;B cell receptor signaling pathway
• Cellular component: extracellular region;nucleoplasm;nucleolus;azurophil granule lumen;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: DNA binding;protein binding