PTCHD3

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	2 clinvar	3
missense			67 clinvar	6 clinvar	5 clinvar	78
nonsense				1 clinvar		1
start loss						0
frameshift					1 clinvar	1
splice donor/acceptor (+/-2bp)						0
Total	0	0	67	8	8	83

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001034842.5	RefSeq	NP_001030014.2	4	Standard
ENST00000642324.1	Ensembl	ENSP00000495205.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatid development

Molecular Function

molecular_function

Cellular Component

cellular_component
integral component of membrane
sperm midpiece

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000438700
Coding exons: 4
Length: 16182
Individuals with no LoFs: 58078
Homozygous LoFs: 12613
Heterozygous LoFs: 55052
Defined: 125743
p: 0.320

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.360	468	447	1.05	0.0000267	4991
Missense (PolyPhen)		107	98.865	1.0823		1220
Synonymous	-0.660	214	202	1.06	0.0000145	1524
Loss of Function	0.867	17	21.3	0.797	0.00000101	255

Population LoF Frequency

Population	CAF	p-value	Status
African	0.29	0.30	notable
Latino/Admixed American	0.25	0.25	notable
Ashkenazi Jewish	0.37	0.37	notable
East Asian	0.17	0.16	notable
Finnish	0.30	0.30	notable
European (Non-Finnish)	0.38	0.38	notable
South Asian	0.33	0.33	notable
Other	0.34	0.33	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in sperm development or sperm function. {ECO:0000269|PubMed:17904097}.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.153
RVIS EVS: 3.16
RVIS percentile EVS: 99.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0393

Gene Damage Prediction

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