UMODL1

uromodulin like 1

Basic information

Region (hg38): 21:42062958-42143453

Links

ENSG00000177398 ∙ NCBI:89766 ∙ OMIM:613859 ∙ HGNC:12560 ∙ Uniprot:Q5DID0 ∙ 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 UMODL1 gene.

• Inborn genetic diseases (97 variants)
• not provided (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UMODL1 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				9	3	12
missense			84	15		99
nonsense						0
start loss			1			1
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				1	1	2
Total	0	0	85	25	4

Variants in UMODL1

This is a list of pathogenic ClinVar variants found in the UMODL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-42071330-C-T		not specified	Likely benign (Oct 12, 2021)
21-42076131-G-A		not specified	Uncertain significance (Oct 26, 2022)
21-42076147-G-A		not specified	Uncertain significance (Sep 27, 2021)
21-42076183-C-T			Likely benign (May 01, 2022)
21-42076196-G-A		not specified	Uncertain significance (Aug 17, 2022)
21-42076220-G-A		not specified	Uncertain significance (Dec 19, 2022)
21-42076222-A-T		not specified	Uncertain significance (Aug 02, 2022)
21-42076230-G-A		not specified	Uncertain significance (Apr 11, 2023)
21-42084098-G-A		not specified	Likely benign (Dec 07, 2023)
21-42084098-G-C		not specified	Likely benign (Jul 14, 2021)
21-42084140-C-A		not specified	Uncertain significance (May 08, 2023)
21-42084184-T-A			Likely benign (Apr 01, 2023)
21-42084188-C-T			Likely benign (Dec 01, 2023)
21-42084191-G-A		not specified	Uncertain significance (Feb 23, 2023)
21-42084213-G-C		not specified	Uncertain significance (Oct 30, 2023)
21-42084215-G-A		not specified	Uncertain significance (Nov 17, 2022)
21-42085306-C-G		not specified	Uncertain significance (Jan 19, 2024)
21-42085315-C-T		not specified	Likely benign (May 24, 2023)
21-42085324-A-G		not specified	Uncertain significance (Nov 18, 2022)
21-42085369-T-G		not specified	Uncertain significance (Jun 12, 2023)
21-42085389-C-A		not specified	Uncertain significance (Oct 04, 2022)
21-42088313-C-A		not specified	Uncertain significance (Nov 18, 2022)
21-42088317-G-A		not specified	Uncertain significance (May 10, 2022)
21-42088324-A-G		not specified	Likely benign (Jun 06, 2023)
21-42088327-G-A		not specified	Likely benign (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UMODL1	protein_coding	protein_coding	ENST00000408989	21	80496

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.29e-36	0.0000933	124080	19	1649	125748	0.00665

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.324	906	879	1.03	0.0000536	9376
Missense in Polyphen		231	219.39	1.0529		2192
Synonymous	-0.818	409	388	1.05	0.0000270	3008
Loss of Function	0.734	58	64.4	0.901	0.00000337	657

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0493	0.0469
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0294	0.0286
Finnish	0.000511	0.000508
European (Non-Finnish)	0.00125	0.00123
Middle Eastern	0.0294	0.0286
South Asian	0.00348	0.00340
Other	0.00398	0.00392

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.137
• rvis_EVS: 3.92
• rvis_percentile_EVS: 99.65

Haploinsufficiency Scores

• pHI: 0.143
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Umodl1

Gene ontology

• Biological process: single fertilization;negative regulation of peptidase activity;regulation of gene expression;regulation of apoptotic process;multicellular organismal reproductive process;adipose tissue development;cellular response to gonadotropin-releasing hormone;regulation of ovarian follicle development
• Cellular component: extracellular space;cytoplasm;external side of plasma membrane;integral component of membrane
• Molecular function: calcium ion binding;peptidase inhibitor activity