LRRC74A

Gene

leucine rich repeat containing 74A

Gene summary

No gene description available in the current model. Review primary literature for detailed gene function and characteristics.

Previous symbols:

C14orf166B
LRRC74

MANE transcript

NM_001385106.1

Inheritance

—

ClinVar variants

P:1U:69B:7

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 0.89

Max pathogenic AF

—

Genomic locus

chr14:76,826,372-76,870,304

External References & Databases

Ensembl (ENSG00000100565)

Transcript & Mutation Effects

hg38 • Region Span ~43.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LRRC74A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 3

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001385106.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		1 clinvar	2
missense			67 clinvar	6 clinvar		73
nonsense						0
start loss						0
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	1	69	6	1	77

Highest pathogenic variant AF is 6.8500094e-7

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001385106.1	RefSeq	NP_001372035.1	14	MANE Select
ENST00000689127.1	Ensembl	ENSP00000509938.1	14	MANE Select
NM_001385107.1	RefSeq	NP_001372036.1	14	Standard
NM_001385108.1	RefSeq	NP_001372037.1	12	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393774
Coding exons: 14
Length: 43931
Individuals with no LoFs: 125397
Homozygous LoFs: 0
Heterozygous LoFs: 196
Defined: 125593
p: 0.000781

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0633	267	264	1.01	0.0000138	3218
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00082	0.00074	rare
Latino/Admixed American	0.00077	0.00075	rare
Ashkenazi Jewish	0.0010	0.00099	notable
East Asian	0.0021	0.0021	notable
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00080	0.00076	rare
South Asian	0.00063	0.00062	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.18
RVIS percentile EVS: 40.56

Essentials

Essential (gene trap): N