HHIPL1

HHIP like 1, the group of Scavenger receptor cysteine rich domain containing

Basic information

Region (hg38): 14:99645128-99680569

Previous symbols: [ "KIAA1822" ]

Links

ENSG00000182218 ∙ NCBI:84439 ∙ ∙ HGNC:19710 ∙ Uniprot:Q96JK4 ∙ 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 HHIPL1 gene.

• Inborn genetic diseases (46 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HHIPL1 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				1		1
missense			45	1		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	2	0

Variants in HHIPL1

This is a list of pathogenic ClinVar variants found in the HHIPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-99645242-T-G		not specified	Uncertain significance (Mar 24, 2023)
14-99645370-G-A		not specified	Uncertain significance (Mar 12, 2024)
14-99645447-G-T		not specified	Uncertain significance (Nov 08, 2022)
14-99652237-A-C		not specified	Uncertain significance (Mar 11, 2024)
14-99652239-G-A		not specified	Uncertain significance (Jun 13, 2022)
14-99652257-G-A		not specified	Uncertain significance (Dec 19, 2022)
14-99652260-G-A		not specified	Uncertain significance (Apr 22, 2022)
14-99652273-C-T		not specified	Uncertain significance (Jul 14, 2021)
14-99652275-C-A		not specified	Uncertain significance (Oct 03, 2022)
14-99652281-C-A		not specified	Uncertain significance (Apr 28, 2023)
14-99652335-C-T		not specified	Uncertain significance (Nov 10, 2022)
14-99652338-G-A		not specified	Uncertain significance (Mar 06, 2023)
14-99652347-C-T		not specified	Uncertain significance (Feb 22, 2023)
14-99652429-C-T		not specified	Uncertain significance (Feb 16, 2023)
14-99652542-G-A		not specified	Uncertain significance (Sep 14, 2022)
14-99652557-G-A		not specified	Uncertain significance (Jul 05, 2023)
14-99652590-C-T		not specified	Uncertain significance (Sep 13, 2023)
14-99652591-G-A		not specified	Uncertain significance (Feb 28, 2024)
14-99652713-C-T		not specified	Uncertain significance (May 23, 2023)
14-99652785-G-T		not specified	Uncertain significance (Jan 03, 2024)
14-99657012-G-T		not specified	Uncertain significance (Feb 02, 2024)
14-99657044-G-C		not specified	Uncertain significance (May 22, 2023)
14-99657058-G-A		not specified	Uncertain significance (Sep 12, 2023)
14-99657070-T-C		not specified	Uncertain significance (May 10, 2022)
14-99657097-G-A		not specified	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HHIPL1	protein_coding	protein_coding	ENST00000330710	9	35460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000237	0.979	125673	1	74	125748	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	339	432	0.785	0.0000301	4981
Missense in Polyphen		174	222.01	0.78375		2314
Synonymous	0.788	184	198	0.929	0.0000153	1649
Loss of Function	2.12	13	24.3	0.535	0.00000104	310

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000416	0.000416
Ashkenazi Jewish	0.00	0.00
East Asian	0.00169	0.00169
Finnish	0.00	0.00
European (Non-Finnish)	0.000194	0.000193
Middle Eastern	0.00169	0.00169
South Asian	0.000294	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.379
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.148

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hhipl1
• Phenotype: renal/urinary system phenotype; skeleton phenotype; limbs/digits/tail phenotype

Zebrafish Information Network

• Gene name: hhipl1
• Affected structure: ventricular system
• Phenotype tag: abnormal
• Phenotype quality: hydrocephalic

Gene ontology

• Biological process: receptor-mediated endocytosis;biological_process
• Cellular component: cellular_component;extracellular region;membrane
• Molecular function: molecular_function;catalytic activity;scavenger receptor activity