NSD3

nuclear receptor binding SET domain protein 3, the group of Lysine methyltransferases|PWWP domain containing|PHD finger proteins|SET domain containing

Basic information

Region (hg38): 8:38269704-38382272

Previous symbols: [ "WHSC1L1" ]

Links

ENSG00000147548 ∙ NCBI:54904 ∙ OMIM:607083 ∙ HGNC:12767 ∙ Uniprot:Q9BZ95 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 13.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_023034.2	NP_075447.1	23	yes	-
ENST00000317025.13	ENSP00000313983.7	23	yes	-
NM_017778.3	NP_060248.2	9	-	-
ENST00000316985.7	ENSP00000313410.3	9	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NSD3 gene.

• not_specified (127 variants)
• not_provided (11 variants)
• NSD3-related_disorder (10 variants)
• Nut_midline_carcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NSD3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_023034.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	10	2	13
missense			137	3	4	144
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3			3
Total	0	0	141	13	6

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NSD3	protein_coding	protein_coding	ENST00000317025	23	112576

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.73	483	775	0.623	0.0000408	9463
Missense in Polyphen		139	335.61	0.41418		3999
Synonymous	1.47	247	278	0.888	0.0000153	2639
Loss of Function	7.44	5	74.1	0.0674	0.00000398	928

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000561	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000540	0.0000527
Middle Eastern	0.0000561	0.0000544
South Asian	0.0000373	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone methyltransferase. Preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation, while 'Lys-27' is a mark for transcriptional repression. {ECO:0000269|PubMed:16682010}.
• Disease: DISEASE: Note=A chromosomal aberration involving NSD3 is found in childhood acute myeloid leukemia. Translocation t(8;11)(p11.2;p15) with NUP98. {ECO:0000269|PubMed:11986249}.
• Pathway: Lysine degradation - Homo sapiens (human);PKMTs methylate histone lysines;Chromatin modifying enzymes;Lysine metabolism;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.0998

Intolerance Scores

• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.93

Essentials

• essential_gene_gene_trap: N

Gene ontology

• Biological process: regulation of transcription, DNA-templated;histone methylation;histone lysine methylation;positive regulation of transcription, DNA-templated;positive regulation of histone H3-K36 trimethylation
• Cellular component: chromatin;nucleus;nucleoplasm;chromosome
• Molecular function: transcription coactivator activity;protein binding;histone-lysine N-methyltransferase activity;metal ion binding;histone methyltransferase activity (H3-K36 specific)