PROSER1

protein-coding

proline and serine rich 1

Gene summary

This gene encodes a conserved protein containing proline and serine rich regions. These regions may be important in protein-protein interactions. [provided by RefSeq, Aug 2012]

Previous symbols:

C13orf23

MANE transcript

NM_025138.5

Inheritance

ClinVar variants

U:145B:12

Top phenotype

PROSER1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr13:39,009,865-39,038,089

External References & Databases

Ensembl (ENSG00000120685)

Transcript & Mutation Effects

hg38 • Region Span ~28.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

syndromic diseaseLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0002254

Submitter: PanelApp Australia

neurodevelopmental disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: G2P

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PROSER1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 131

not providedTotal: 8

PROSER1-related disorderTotal: 2

PROSER1-related Neurodevelopmental disordersTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025138.5. 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			4 clinvar	4 clinvar	2 clinvar	10
missense			132 clinvar	5 clinvar	1 clinvar	138
nonsense			2 clinvar			2
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	145	9	3	157

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025138.5	RefSeq	NP_079414.3	13	MANE Select
ENST00000352251.8	Ensembl	ENSP00000332034.4	13	MANE Select
NM_170719.4	RefSeq	NP_733837.2	12	Standard
ENST00000418503.1	Ensembl	ENSP00000413879.1	4	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000352251
Coding exons: 13
Length: 28250
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 26
Defined: 125748
p: 0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.138	492	501	0.983	0.0000258	5881
Missense (PolyPhen)		160	183.87	0.87018		2273
Synonymous	-0.779	218	204	1.07	0.0000114	2212
Loss of Function	4.10	6	30.4	0.197	0.00000157	422

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00071	0.00071	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0957

Intolerance Scores

RVIS EVS: -0.17
RVIS percentile EVS: 40.65

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium