KDM7A

lysine demethylase 7A, the group of PHD finger proteins|Lysine demethylases

Basic information

Region (hg38): 7:140084745-140176983

Previous symbols: [ "JHDM1D" ]

Links

ENSG00000006459 ∙ NCBI:80853 ∙ OMIM:619640 ∙ HGNC:22224 ∙ Uniprot:Q6ZMT4 ∙ 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 KDM7A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KDM7A 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in KDM7A

This is a list of pathogenic ClinVar variants found in the KDM7A region.

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

Position	Type	Phenotype	Significance	ClinVar
7-140091872-G-A		not specified	Uncertain significance (Oct 11, 2023)
7-140091932-G-A		not specified	Uncertain significance (Sep 14, 2023)
7-140094076-T-G		not specified	Uncertain significance (Feb 05, 2024)
7-140094079-C-G		not specified	Uncertain significance (Jun 19, 2024)
7-140096647-C-T		not specified	Uncertain significance (Jun 22, 2024)
7-140096686-G-T		not specified	Uncertain significance (Mar 07, 2024)
7-140096953-C-T		not specified	Uncertain significance (Oct 26, 2022)
7-140096986-G-A		not specified	Uncertain significance (Jan 19, 2022)
7-140097008-C-G		not specified	Uncertain significance (Sep 22, 2023)
7-140097549-G-A		not specified	Uncertain significance (May 23, 2023)
7-140097556-A-T		not specified	Uncertain significance (Jan 03, 2022)
7-140099947-G-A		not specified	Uncertain significance (Jul 20, 2022)
7-140102036-T-C		not specified	Uncertain significance (Apr 23, 2024)
7-140102123-G-T		not specified	Uncertain significance (Oct 18, 2021)
7-140111105-C-T		not specified	Uncertain significance (Jun 04, 2024)
7-140111152-G-T		not specified	Uncertain significance (Feb 28, 2024)
7-140113552-G-T		not specified	Uncertain significance (Jan 22, 2024)
7-140124692-A-G		not specified	Uncertain significance (May 24, 2024)
7-140124707-G-C		not specified	Uncertain significance (Feb 27, 2024)
7-140124746-T-G		not specified	Uncertain significance (Dec 16, 2022)
7-140126809-A-G		not specified	Uncertain significance (May 01, 2024)
7-140126822-T-C		not specified	Uncertain significance (Sep 13, 2023)
7-140127446-T-C		not specified	Uncertain significance (Apr 17, 2024)
7-140127526-G-A		not specified	Uncertain significance (Nov 29, 2023)
7-140127528-C-T		not specified	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KDM7A	protein_coding	protein_coding	ENST00000397560	20	92290

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000142	124783	0	11	124794	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.46	334	487	0.686	0.0000240	6217
Missense in Polyphen		73	178.6	0.40874		2274
Synonymous	0.175	169	172	0.983	0.00000878	1718
Loss of Function	5.89	6	51.7	0.116	0.00000277	626

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000296	0.0000296
Ashkenazi Jewish	0.000105	0.0000993
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000447	0.0000441
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone demethylase required for brain development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3 and monomethylated histone H4 'Lys-20' residue (H4K20Me1), thereby playing a central role in histone code. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: in presence of H3K4me3, it has no demethylase activity toward H3K9me2, while it has high activity toward H3K27me2. Demethylates H3K9me2 in absence of H3K4me3. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate. {ECO:0000269|PubMed:20023638, ECO:0000269|PubMed:20194436, ECO:0000269|PubMed:20622853}.
• Pathway: Disease;HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction (Consensus)

Recessive Scores

• pRec: 0.0936

Intolerance Scores

• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.56

Haploinsufficiency Scores

• pHI: 0.174
• hipred: Y
• hipred_score: 0.728
• ghis: 0.463

Essentials

• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kdm7a
• Phenotype: hematopoietic system phenotype; limbs/digits/tail phenotype; skeleton phenotype; immune system phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: midbrain development;histone H3-K9 demethylation;histone H4-K20 demethylation;positive regulation of transcription, DNA-templated;oxidation-reduction process;histone H3-K36 demethylation;histone H3-K27 demethylation
• Cellular component: nucleus;nucleoplasm;nucleolus
• Molecular function: iron ion binding;zinc ion binding;2-oxoglutarate-dependent dioxygenase activity;histone demethylase activity;histone demethylase activity (H3-K9 specific);methylated histone binding;histone demethylase activity (H4-K20 specific);histone demethylase activity (H3-K36 specific);histone demethylase activity (H3-K27 specific)