MSANTD2

Myb/SANT DNA binding domain containing 2, the group of Myb/SANT domain containing

Basic information

Region (hg38): 11:124766498-124800706

Previous symbols: [ "C11orf61" ]

Links

ENSG00000120458 ∙ NCBI:79684 ∙ ∙ HGNC:26266 ∙ Uniprot:Q6P1R3 ∙ 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 MSANTD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSANTD2 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in MSANTD2

This is a list of pathogenic ClinVar variants found in the MSANTD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-124767331-C-T		not specified	Uncertain significance (Mar 25, 2024)
11-124767539-C-T		not specified	Uncertain significance (Feb 05, 2024)
11-124767705-C-T		not specified	Uncertain significance (Aug 04, 2023)
11-124767960-T-C		not specified	Uncertain significance (Mar 29, 2022)
11-124774786-G-C		not specified	Likely benign (Apr 07, 2023)
11-124799875-A-C		not specified	Uncertain significance (Mar 01, 2023)
11-124799893-G-C		not specified	Uncertain significance (Sep 07, 2022)
11-124799905-T-C		not specified	Uncertain significance (Dec 14, 2021)
11-124799968-C-A		not specified	Uncertain significance (Feb 06, 2024)
11-124800106-G-C		not specified	Uncertain significance (Sep 16, 2021)
11-124800133-G-A		not specified	Uncertain significance (Feb 05, 2024)
11-124800154-G-A		not specified	Uncertain significance (Oct 12, 2022)
11-124800178-A-C		not specified	Uncertain significance (Aug 04, 2021)
11-124800193-G-A		not specified	Uncertain significance (Sep 16, 2021)
11-124800193-G-C		not specified	Uncertain significance (Jul 11, 2022)
11-124800221-T-C		not specified	Uncertain significance (Apr 07, 2023)
11-124800307-G-C		not specified	Uncertain significance (Aug 31, 2023)
11-124800317-C-T		not specified	Uncertain significance (Mar 25, 2024)
11-124800353-G-A		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSANTD2	protein_coding	protein_coding	ENST00000239614	4	34176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.903	0.0972	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.30	155	259	0.598	0.0000130	3218
Missense in Polyphen		48	104.16	0.46081		1344
Synonymous	1.46	84	103	0.817	0.00000517	1022
Loss of Function	3.61	3	20.7	0.145	0.00000114	235

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000920	0.0000907
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.496
• hipred: Y
• hipred_score: 0.673
• ghis: 0.651

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Msantd2