LRRC74A

leucine rich repeat containing 74A

Basic information

Region (hg38): 14:76826372-76870304

Previous symbols: [ "C14orf166B", "LRRC74" ]

Links

ENSG00000100565 ∙ NCBI:145497 ∙ ∙ HGNC:23346 ∙ Uniprot:Q0VAA2 ∙ 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 LRRC74A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LRRC74A 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			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	32	2	2

Variants in LRRC74A

This is a list of pathogenic ClinVar variants found in the LRRC74A region.

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

Position	Type	Phenotype	Significance	ClinVar
14-76826505-C-G		not specified	Uncertain significance (Dec 27, 2023)
14-76826563-G-T		not specified	Uncertain significance (Jun 05, 2024)
14-76826568-C-T		not specified	Uncertain significance (May 13, 2022)
14-76828350-G-A		not specified	Uncertain significance (May 03, 2023)
14-76828390-A-G		not specified	Uncertain significance (Apr 09, 2022)
14-76831304-G-A		not specified	Uncertain significance (Jun 02, 2023)
14-76831311-A-G		not specified	Uncertain significance (Nov 20, 2023)
14-76831331-G-A		not specified	Uncertain significance (Oct 02, 2023)
14-76831345-G-C		not specified	Uncertain significance (Apr 12, 2023)
14-76831347-G-A		not specified	Uncertain significance (Apr 23, 2024)
14-76836214-T-A		not specified	Uncertain significance (Apr 15, 2024)
14-76836295-A-C		not specified	Uncertain significance (May 30, 2023)
14-76837902-G-A		not specified	Uncertain significance (Feb 10, 2022)
14-76837958-C-A		not specified	Uncertain significance (Jan 03, 2024)
14-76852382-A-G		not specified	Uncertain significance (Jan 08, 2024)
14-76852383-C-T		not specified	Uncertain significance (Feb 17, 2023)
14-76853223-T-G		not specified	Uncertain significance (Jul 14, 2021)
14-76853232-C-G		not specified	Uncertain significance (Aug 08, 2023)
14-76853298-G-T		not specified	Uncertain significance (Jan 09, 2024)
14-76853304-A-G		not specified	Uncertain significance (Mar 15, 2024)
14-76853307-G-A		not specified	Uncertain significance (Feb 28, 2023)
14-76853315-G-T		not specified	Uncertain significance (Oct 20, 2021)
14-76853316-T-C		not specified	Likely benign (Sep 25, 2023)
14-76853330-G-A		not specified	Likely benign (Jan 03, 2024)
14-76853350-T-C			Benign (Aug 03, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LRRC74A	protein_coding	protein_coding	ENST00000393774	14	43931

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.55e-14	0.0499	125397	0	196	125593	0.000781

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0633	267	264	1.01	0.0000138	3218
Missense in Polyphen		61	57.645	1.0582		764
Synonymous	-0.258	112	109	1.03	0.00000648	907
Loss of Function	0.538	23	26.0	0.886	0.00000139	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00158	0.00151
Ashkenazi Jewish	0.00101	0.000994
East Asian	0.00213	0.00212
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000797	0.000758
Middle Eastern	0.00213	0.00212
South Asian	0.000625	0.000621
Other	0.000501	0.000490

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.56

Haploinsufficiency Scores

• pHI: 0.343
• hipred: N
• hipred_score: 0.123
• ghis: 0.451

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Lrrc74a