PKHD1L1

PKHD1 like 1, the group of IPT domain containing

Basic information

Region (hg38): 8:109362460-109537207

Links

ENSG00000205038 ∙ NCBI:93035 ∙ OMIM:607843 ∙ HGNC:20313 ∙ Uniprot:Q86WI1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Deafness, autosomal recessive 124	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may improve outcomes, including speech and language development	Audiologic/Otolaryngologic	38459354

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PKHD1L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PKHD1L1 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				3	2	5
missense			247	10	4	261
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1		1	2
splice region						0
non coding						0
Total	0	0	248	13	7

Variants in PKHD1L1

This is a list of pathogenic ClinVar variants found in the PKHD1L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-109362587-C-T		not specified	Uncertain significance (May 24, 2023)
8-109362612-G-A		not specified	Uncertain significance (May 12, 2024)
8-109381427-G-A		not specified	Uncertain significance (Mar 07, 2024)
8-109381437-A-T		not specified	Uncertain significance (Apr 26, 2024)
8-109381444-T-G		not specified	Uncertain significance (Mar 01, 2023)
8-109381445-C-G		not specified	Uncertain significance (Dec 15, 2022)
8-109381488-T-A		not specified	Uncertain significance (Apr 18, 2023)
8-109382539-G-A		Autosomal recessive nonsyndromic hearing loss 124	Pathogenic (Apr 23, 2024)
8-109382570-A-T		not specified	Uncertain significance (Sep 01, 2021)
8-109384089-C-T		not specified	Uncertain significance (Jan 19, 2024)
8-109384122-C-A		not specified	Uncertain significance (Sep 06, 2022)
8-109385576-T-C		not specified	Uncertain significance (Jan 05, 2022)
8-109388541-C-T		not specified	Uncertain significance (Mar 14, 2023)
8-109389079-A-T		not specified	Uncertain significance (May 26, 2024)
8-109389083-G-C		not specified	Uncertain significance (Dec 05, 2022)
8-109389129-G-A		not specified	Uncertain significance (Apr 07, 2022)
8-109390472-A-G		not specified	Uncertain significance (Jan 22, 2024)
8-109390482-A-G		not specified	Likely benign (Jan 03, 2024)
8-109394434-G-A		not specified	Likely benign (Oct 06, 2023)
8-109394456-A-G		not specified	Uncertain significance (Jan 04, 2024)
8-109396027-A-T		not specified	Uncertain significance (Mar 29, 2022)
8-109396051-A-G		not specified	Uncertain significance (Jan 23, 2024)
8-109396075-C-T		not specified	Uncertain significance (Mar 19, 2024)
8-109396085-A-G		not specified	Uncertain significance (Aug 10, 2021)
8-109396092-C-A		not specified	Uncertain significance (Feb 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PKHD1L1	protein_coding	protein_coding	ENST00000378402	78	167854

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.37e-109	4.94e-15	105692	1486	17698	124876	0.0800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.719	2145	2.05e+3	1.04	0.000100	27569
Missense in Polyphen		586	583.56	1.0042		7591
Synonymous	-0.630	757	735	1.03	0.0000383	8193
Loss of Function	0.857	174	187	0.932	0.00000959	2493

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.287	0.287
Ashkenazi Jewish	0.0169	0.0167
East Asian	0.0250	0.0242
Finnish	0.0735	0.0719
European (Non-Finnish)	0.0653	0.0638
Middle Eastern	0.0250	0.0242
South Asian	0.0667	0.0640
Other	0.0719	0.0685

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.0530
• rvis_EVS: 5.45
• rvis_percentile_EVS: 99.85

Haploinsufficiency Scores

• pHI: 0.384
• hipred: N
• hipred_score: 0.199
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.108

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pkhd1l1

Gene ontology

• Biological process: immune response
• Cellular component: extracellular space;cytosol;cilium;integral component of membrane
• Molecular function: signaling receptor activity