MSANTD1

Myb/SANT DNA binding domain containing 1, the group of Myb/SANT domain containing

Basic information

Region (hg38): 4:3244369-3271738

Previous symbols: [ "C4orf44" ]

Links

ENSG00000188981 ∙ NCBI:345222 ∙ ∙ HGNC:33741 ∙ Uniprot:Q6ZTZ1 ∙ 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 MSANTD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSANTD1 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in MSANTD1

This is a list of pathogenic ClinVar variants found in the MSANTD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-3249229-C-T		not specified	Uncertain significance (Feb 26, 2024)
4-3249238-G-A		not specified	Likely benign (Dec 28, 2022)
4-3249242-C-A		not specified	Uncertain significance (Oct 05, 2021)
4-3249260-C-T		not specified	Uncertain significance (Jan 06, 2023)
4-3249266-C-G		not specified	Uncertain significance (Jun 02, 2023)
4-3249279-C-T		not specified	Likely benign (Jun 21, 2023)
4-3249286-G-A		not specified	Likely benign (May 20, 2024)
4-3249310-G-A		not specified	Uncertain significance (Jun 06, 2023)
4-3249319-G-A		not specified	Uncertain significance (Oct 16, 2023)
4-3249332-C-T		not specified	Uncertain significance (Sep 25, 2024)
4-3249487-C-T		not specified	Uncertain significance (Jul 20, 2021)
4-3253296-A-G		not specified	Uncertain significance (Jun 03, 2022)
4-3253361-T-C		not specified	Uncertain significance (Dec 27, 2023)
4-3253410-A-G		not specified	Uncertain significance (Oct 16, 2023)
4-3253421-G-A		not specified	Uncertain significance (Apr 20, 2023)
4-3253427-C-T		not specified	Uncertain significance (Dec 26, 2023)
4-3253428-G-A		not specified	Uncertain significance (Jun 02, 2023)
4-3253433-G-A		not specified	Uncertain significance (Jun 12, 2023)
4-3253435-G-T		not specified	Uncertain significance (Sep 23, 2023)
4-3253442-C-T		not specified	Uncertain significance (Sep 30, 2024)
4-3253448-G-T		not specified	Uncertain significance (Aug 10, 2024)
4-3253449-A-C		not specified	Uncertain significance (Aug 10, 2024)
4-3255736-G-A		not specified	Uncertain significance (Sep 20, 2024)
4-3255739-C-T		not specified	Uncertain significance (May 22, 2024)
4-3255779-G-T		not specified	Uncertain significance (Mar 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSANTD1	protein_coding	protein_coding	ENST00000438480	3	27370

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.805	0.194	125675	0	4	125679	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.746	157	186	0.846	0.0000136	1785
Missense in Polyphen		49	71.376	0.68651		655
Synonymous	0.0246	89	89.3	0.997	0.00000760	556
Loss of Function	2.60	1	9.76	0.102	4.18e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000363	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: 0.0895

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.292
• ghis: 0.415

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: Msantd1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: positive regulation of transcription, DNA-templated
• Cellular component: nuclear body