Is KY p.Arg187= (c.561C>T) pathogenic?

KY p.Arg187= (c.561C>T) is classified Likely benign in KY (ClinVar, Single submitter, 2 submitters; last evaluated 2019-12-31). Rare (popmax 0.171%, afr).

How common is KY p.Arg187= (c.561C>T) in the general population?

KY p.Arg187= (c.561C>T) is rare (popmax 0.171%, afr) (gnomAD).

KY p.Arg187=

c.561C>T · rs371587266 · VCV735946

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.171%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -8.7	GERP -2.6
Overall
CADD	1.171	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.171% African / African-American · 128/75,050 alleles

Filtering AF 0.146% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.137%

Overall 0.0126% 204/1,613,704 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.171%	586
East Asian	0.00669%	14,958
Remaining individualsnot grpmax-eligible	0.0064%	15,619
European (non-Finnish)	0.00542%	18,434
Admixed American	0.00333%	30,000
South Asian	0.0033%	30,325

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: KY
Protein: p.Arg187=
Coding: c.561C>T
MANE Select: NM_001353108 · reported on NM_178554
dbSNP: rs371587266
Type: single nucleotide variant
Location: chr3:134620780 (GRCh38)

Full KY gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ky-p-arg187 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown