HSPA4L

heat shock protein family A (Hsp70) member 4 like, the group of Heat shock 70kDa proteins

Basic information

Region (hg38): 4:127781820-127840733

Links

ENSG00000164070 ∙ NCBI:22824 ∙ OMIM:619077 ∙ HGNC:17041 ∙ Uniprot:O95757 ∙ 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 HSPA4L gene.

• Inborn genetic diseases (28 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HSPA4L 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				2	2	4
missense			25	4		29
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	6	2

Variants in HSPA4L

This is a list of pathogenic ClinVar variants found in the HSPA4L region.

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

Position	Type	Phenotype	Significance	ClinVar
4-127795775-C-T		not specified	Uncertain significance (Feb 10, 2023)
4-127795779-C-T			Benign (Jul 31, 2018)
4-127795781-T-C		not specified	Uncertain significance (Apr 12, 2023)
4-127795854-G-T		not specified	Uncertain significance (Nov 18, 2022)
4-127795855-A-T		not specified	Uncertain significance (Nov 18, 2022)
4-127795874-T-C		not specified	Uncertain significance (Dec 13, 2023)
4-127795895-G-C		not specified	Uncertain significance (Dec 14, 2022)
4-127798591-G-A		not specified	Uncertain significance (Jan 30, 2024)
4-127798599-G-C		not specified	Uncertain significance (May 26, 2023)
4-127798620-A-G		not specified	Uncertain significance (May 17, 2023)
4-127798695-G-C		not specified	Uncertain significance (Oct 26, 2022)
4-127801794-C-T			Likely benign (Feb 01, 2023)
4-127801834-G-T		not specified	Uncertain significance (Nov 03, 2022)
4-127801838-C-G		not specified	Uncertain significance (Jul 17, 2023)
4-127803759-G-A		not specified	Uncertain significance (Feb 21, 2024)
4-127805153-A-G		not specified	Uncertain significance (Oct 12, 2022)
4-127805787-G-A		not specified	Uncertain significance (Feb 15, 2023)
4-127808025-C-T		not specified	Uncertain significance (Mar 31, 2022)
4-127808093-A-C		not specified	Uncertain significance (Aug 02, 2023)
4-127811460-T-A		not specified	Uncertain significance (Aug 14, 2023)
4-127811540-C-A		not specified	Uncertain significance (Jul 12, 2022)
4-127811573-C-T			Likely benign (Feb 01, 2023)
4-127811574-G-C		not specified	Uncertain significance (Nov 17, 2022)
4-127811635-T-C		not specified	Uncertain significance (Nov 17, 2023)
4-127818394-A-G		not specified	Uncertain significance (May 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HSPA4L	protein_coding	protein_coding	ENST00000296464	19	58913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.95e-7	1.00	125705	0	41	125746	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	372	431	0.864	0.0000208	5576
Missense in Polyphen		109	140.2	0.77747		1731
Synonymous	1.27	128	148	0.868	0.00000738	1479
Loss of Function	3.53	18	43.0	0.419	0.00000215	580

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000384	0.000375
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.000402	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possesses chaperone activity in vitro where it inhibits aggregation of citrate synthase. {ECO:0000250}.
• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Regulation of HSF1-mediated heat shock response;Cellular responses to stress;Cellular responses to external stimuli;Cellular response to heat stress (Consensus)

Recessive Scores

• pRec: 0.162

Intolerance Scores

• loftool: 0.842
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.51

Haploinsufficiency Scores

• pHI: 0.632
• hipred: N
• hipred_score: 0.492
• ghis: 0.485

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.351

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hspa4l
• Phenotype: renal/urinary system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein folding;response to unfolded protein
• Cellular component: nucleus;cytoplasm;cytosol
• Molecular function: ATP binding