YLPM1

Chr 14

YLP motif containing 1

Also known as: C14orf170, PPP1R169, ZAP113, ZAP3

NCBI Gene: 56252 ENSG00000119596 UniProt: P49750 OMIM: 619766

Enables RNA binding activity. Predicted to be involved in regulation of telomere maintenance. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Located in nuclear speck. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.26

Clinical Summary— YLPM1

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

343 VUS of 396 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.26LOEUF

pLI 1.000

Z-score 7.72

OE 0.18 (0.12–0.26)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

0.77Z-score

OE missense 0.94 (0.89–0.98)

1092 obs / 1165.8 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.18 (0.12–0.26)

0≤0.351.4

Missense OE?0.94 (0.89–0.98)

0≤0.61.4

Synonymous OE?1.04

0≤1.21.6

LoF obs/exp: 18 / 102.2Missense obs/exp: 1092 / 1165.8Syn Z: -0.65

This gene — mechanism propensity

0.19100th %ile

GOF

0.13100th %ile

LOF

0.84top 5%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.26

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

396 submitted variants in ClinVar

ClinVar

Classification Summary

VUS343

Likely Benign12

Benign3

343

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	1	342	0	343
Likely Benign	0	8	4	12
Benign	0	1	2	3
Total	1	351	6	358

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

14 pathogenic / likely-pathogenic (of 18) ClinVar copy-number / structural variants overlap YLPM1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →