MSANTD2

Gene

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

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

C11orf61

MANE transcript

NM_001308027.2

Inheritance

—

ClinVar variants

U:62B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr11:124,766,498-124,800,706

External References & Databases

Ensembl (ENSG00000120458)

Transcript & Mutation Effects

hg38 • Region Span ~34.2 kb

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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 MSANTD2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 59

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001308027.2. 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	1 clinvar		2
missense			60 clinvar	1 clinvar		61
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	62	2	0	64

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001308027.2	RefSeq	NP_001294956.1	4	MANE Select
ENST00000374979.8	Ensembl	ENSP00000364118.3	4	MANE Select
NM_001312919.2	RefSeq	NP_001299848.1	2	Standard
NM_001312920.2	RefSeq	NP_001299849.1	3	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000239614
Coding exons: 4
Length: 34176
Individuals with no LoFs: 125741
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125748
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.30	155	259	0.598	0.0000130	3218
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000063	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.103

Intolerance Scores

RVIS EVS: -0.45
RVIS percentile EVS: 24

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