MSANTD1

protein-coding

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

Gene summary

Predicted to be involved in positive regulation of DNA-templated transcription. Predicted to be active in nuclear body. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C4orf44

MANE transcript

NM_001042690.2

Inheritance

—

ClinVar variants

U:54B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr4:3,244,369-3,271,738

External References & Databases

Ensembl (ENSG00000188981)

Transcript & Mutation Effects

hg38 • Region Span ~27.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to MSANTD1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 57

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001042690.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	2 clinvar		3
missense			53 clinvar	3 clinvar		56
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	54	5	0	59

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001042690.2	RefSeq	NP_001036155.1	3	MANE Select
ENST00000438480.7	Ensembl	ENSP00000411584.2	3	MANE Select
NM_001330620.2	RefSeq	NP_001317549.1	4	Standard
ENST00000505599.5	Ensembl	ENSP00000425405.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of transcription, DNA-templated

Cellular Component

nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000438480
Coding exons: 3
Length: 27370
Individuals with no LoFs: 125675
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125679
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.746	157	186	0.846	0.0000136	1785
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0895

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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