ANTKMT

adenine nucleotide translocase lysine methyltransferase, the group of 7BS protein lysine methyltransferases

Basic information

Region (hg38): 16:720580-722590

Previous symbols: [ "C16orf24", "FAM173A" ]

Links

ENSG00000103254 ∙ NCBI:65990 ∙ OMIM:618566 ∙ HGNC:14152 ∙ Uniprot:Q9BQD7 ∙ 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 ANTKMT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANTKMT 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in ANTKMT

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

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

Position	Type	Phenotype	Significance	ClinVar
16-721300-C-T		not specified	Uncertain significance (Dec 05, 2022)
16-721344-C-G		not specified	Uncertain significance (Feb 28, 2023)
16-721623-G-C		not specified	Uncertain significance (Jan 23, 2024)
16-721811-C-T		not specified	Uncertain significance (Dec 03, 2021)
16-721818-G-T		not specified	Uncertain significance (Feb 27, 2024)
16-721832-C-G		not specified	Uncertain significance (Jun 02, 2024)
16-721906-G-T		not specified	Uncertain significance (Oct 27, 2023)
16-721919-A-G		not specified	Uncertain significance (May 18, 2022)
16-722102-C-T		not specified	Uncertain significance (Jan 06, 2023)
16-722126-C-T		not specified	Uncertain significance (Sep 27, 2021)
16-722313-C-G		not specified	Uncertain significance (Mar 19, 2024)
16-722352-G-A		not specified	Uncertain significance (Feb 06, 2023)
16-722367-C-G		not specified	Uncertain significance (Mar 06, 2023)
16-722384-C-T		not specified	Uncertain significance (Jun 28, 2022)
16-722465-G-T		not specified	Uncertain significance (Oct 03, 2022)
16-722466-G-A		not specified	Uncertain significance (Jun 01, 2023)
16-722474-G-T		not specified	Uncertain significance (Dec 21, 2023)
16-722484-G-A		not specified	Uncertain significance (Aug 12, 2021)
16-722507-G-A		not specified	Uncertain significance (Jul 06, 2021)
16-722510-C-T		not specified	Uncertain significance (Jul 28, 2021)
16-722511-C-T		not specified	Uncertain significance (Jul 14, 2023)
16-722519-G-T		not specified	Uncertain significance (Nov 12, 2021)
16-722529-C-G		not specified	Uncertain significance (Jun 11, 2021)
16-722535-G-T		not specified	Uncertain significance (Feb 15, 2023)
16-722544-C-G		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANTKMT	protein_coding	protein_coding	ENST00000569529	5	2021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000877	0.579	122657	0	5	122662	0.0000204

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.326	111	121	0.917	0.00000830	1394
Missense in Polyphen		43	45.704	0.94084		592
Synonymous	1.37	44	57.2	0.769	0.00000428	537
Loss of Function	0.459	5	6.24	0.802	3.66e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000115	0.000110
Finnish	0.00	0.00
European (Non-Finnish)	0.0000193	0.0000181
Middle Eastern	0.000115	0.000110
South Asian	0.0000341	0.0000330
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionin-dependent protein-lysine N- methyltransferase. {ECO:0000250|UniProtKB:Q6P4H8}.

Recessive Scores

• pRec: 0.112

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.167
• ghis: 0.536

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.547

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam173a

Gene ontology

• Biological process: methylation
• Cellular component: integral component of membrane
• Molecular function: methyltransferase activity