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.

• not_specified (63 variants)
• not_provided (3 variants)

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. These statistics are base on transcript: NM_001385106.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			59	4		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	59	4	1

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