HEATR5A

HEAT repeat containing 5A, the group of Armadillo like helical domain containing

Basic information

Region (hg38): 14:31291787-31420550

Previous symbols: [ "C14orf125" ]

Links

ENSG00000129493 ∙ NCBI:25938 ∙ ∙ HGNC:20276 ∙ Uniprot:Q86XA9 ∙ 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 HEATR5A gene.

• Inborn genetic diseases (99 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HEATR5A 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			96	4		100
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	96	4	0

Variants in HEATR5A

This is a list of pathogenic ClinVar variants found in the HEATR5A region.

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

Position	Type	Phenotype	Significance	ClinVar
14-31293337-A-G		not specified	Uncertain significance (Jun 27, 2022)
14-31293377-C-A		not specified	Uncertain significance (Aug 22, 2023)
14-31293423-C-T		not specified	Uncertain significance (Jul 27, 2021)
14-31293424-G-A		not specified	Uncertain significance (Jan 23, 2023)
14-31293429-T-A		not specified	Uncertain significance (Mar 14, 2023)
14-31293453-A-G		not specified	Uncertain significance (Sep 01, 2021)
14-31293508-C-G		not specified	Uncertain significance (May 25, 2022)
14-31293517-G-A		not specified	Uncertain significance (Mar 04, 2024)
14-31293905-G-C		not specified	Uncertain significance (Oct 06, 2021)
14-31293911-G-T		not specified	Uncertain significance (Mar 21, 2023)
14-31293930-C-T		not specified	Uncertain significance (Apr 25, 2022)
14-31294025-G-C		not specified	Uncertain significance (Nov 09, 2023)
14-31294052-G-A		not specified	Uncertain significance (Feb 14, 2023)
14-31296028-G-T		not specified	Uncertain significance (Dec 02, 2022)
14-31302354-G-A		not specified	Uncertain significance (May 26, 2022)
14-31302373-G-A		not specified	Uncertain significance (Jan 30, 2024)
14-31302397-C-T		not specified	Uncertain significance (Oct 05, 2023)
14-31302429-G-A		not specified	Uncertain significance (Sep 17, 2021)
14-31302447-G-A		not specified	Uncertain significance (Dec 20, 2023)
14-31302478-C-G		not specified	Uncertain significance (Apr 20, 2023)
14-31302494-T-C		not specified	Uncertain significance (Jan 31, 2022)
14-31304943-A-G		not specified	Uncertain significance (Mar 27, 2023)
14-31304979-A-G		not specified	Likely benign (Jun 03, 2022)
14-31304997-G-A		not specified	Uncertain significance (Feb 23, 2023)
14-31305042-G-C		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HEATR5A	protein_coding	protein_coding	ENST00000382464	2	128795

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0547	0.719	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.504	45	55.6	0.810	0.00000282	738
Missense in Polyphen		18	25.347	0.71015		333
Synonymous	1.28	14	21.5	0.650	0.00000107	216
Loss of Function	0.736	2	3.48	0.574	1.45e-7	55

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.229
• ghis: 0.466

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Heatr5a

Gene ontology

• Biological process: endocytosis;protein localization;retrograde transport, endosome to Golgi
• Cellular component: cytosol;endocytic vesicle