DIPK1A

divergent protein kinase domain 1A, the group of divergent protein kinase domain family

Basic information

Region (hg38): 1:92832736-92961522

Previous symbols: [ "FAM69A" ]

Links

ENSG00000154511 ∙ NCBI:388650 ∙ OMIM:614542 ∙ HGNC:32213 ∙ Uniprot:Q5T7M9 ∙ 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 DIPK1A gene.

• Diamond-Blackfan anemia (170 variants)
• Diamond-Blackfan anemia 6 (59 variants)
• not provided (26 variants)
• not specified (16 variants)
• Inborn genetic diseases (8 variants)
• - (4 variants)
• RPL5-related condition (3 variants)
• Diamond-Blackfan anemia 1 (2 variants)
• 17 conditions (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DIPK1A 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	47	16	78	57	9	207
Total	47	16	84	57	9

Variants in DIPK1A

This is a list of pathogenic ClinVar variants found in the DIPK1A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-92833372-A-T		Diamond-Blackfan anemia	Likely benign (Dec 01, 2023)
1-92833378-TTTTC-T		Diamond-Blackfan anemia	Pathogenic (Sep 07, 2022)
1-92833379-T-A		Diamond-Blackfan anemia	Likely pathogenic (May 20, 2020)
1-92833379-T-C		Diamond-Blackfan anemia 6	Uncertain significance (Mar 02, 2018)
1-92833380-T-C		Diamond-Blackfan anemia	Likely benign (Oct 14, 2022)
1-92833381-TC-T		Diamond-Blackfan anemia	Likely benign (Sep 11, 2019)
1-92833382-C-T		Diamond-Blackfan anemia	Likely benign (Jan 03, 2024)
1-92833385-T-C		Diamond-Blackfan anemia • Diamond-Blackfan anemia 6	Likely benign (Oct 05, 2022)
1-92833388-G-A		Diamond-Blackfan anemia	Likely pathogenic (Jul 23, 2023)
1-92833390-GGTTT-G		Diamond-Blackfan anemia	Pathogenic (May 25, 2019)
1-92833391-G-A		Diamond-Blackfan anemia	Likely benign (Jan 24, 2023)
1-92833397-T-TA		Diamond-Blackfan anemia	Pathogenic (Mar 03, 2019)
1-92833403-T-A		Diamond-Blackfan anemia	Likely benign (Jul 12, 2022)
1-92833407-A-T		Diamond-Blackfan anemia	Pathogenic (Oct 22, 2014)
1-92833409-GA-G		Diamond-Blackfan anemia	Pathogenic (May 10, 2018)
1-92833420-A-G		Diamond-Blackfan anemia	Uncertain significance (Jun 04, 2019)
1-92833424-TA-T		Inborn genetic diseases	Pathogenic (Dec 06, 2018)
1-92833429-GAT-G			Pathogenic (Nov 29, 2022)
1-92833433-C-A		Diamond-Blackfan anemia	Pathogenic (Sep 04, 2015)
1-92833433-C-G		Diamond-Blackfan anemia	Pathogenic (Aug 27, 2021)
1-92833436-A-G		Diamond-Blackfan anemia	Likely benign (Jan 19, 2024)
1-92833442-AT-A		Diamond-Blackfan anemia	Pathogenic (Sep 29, 2017)
1-92833452-C-T		Diamond-Blackfan anemia 6 • Diamond-Blackfan anemia	Pathogenic (May 15, 2023)
1-92833453-G-A			Uncertain significance (Aug 24, 2022)
1-92833455-C-T		Diamond-Blackfan anemia	Pathogenic (Jan 28, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DIPK1A	protein_coding	protein_coding	ENST00000370310	5	119334

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.584	0.416	124585	0	7	124592	0.0000281

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.26	120	213	0.564	0.0000102	2818
Missense in Polyphen		35	85.407	0.4098		1109
Synonymous	0.716	66	73.8	0.894	0.00000362	776
Loss of Function	2.97	3	15.7	0.191	6.53e-7	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000691	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000535	0.0000531
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.87

Haploinsufficiency Scores

• pHI: 0.296
• hipred: N
• hipred_score: 0.336
• ghis: 0.446

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Fam69a
• Phenotype: homeostasis/metabolism phenotype