Is KY p.Arg510= (c.1530C>T) pathogenic?

KY p.Arg510= (c.1530C>T) is classified Benign/Likely benign in KY (ClinVar, Multiple submitters, 3 submitters; last evaluated 2021-04-02). Low-frequency (popmax 2.42%, nfe).

How common is KY p.Arg510= (c.1530C>T) in the general population?

KY p.Arg510= (c.1530C>T) is low-frequency (popmax 2.42%, nfe) (gnomAD).

KY p.Arg510=

c.1530C>T · rs35316983 · VCV1300557

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.42%, nfe)

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 0.87	GERP 0.75, phastCons 1
Overall
CADD	6.706	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.42% European (non-Finnish) · 28,524/1,179,860 alleles

Filtering AF 2.39% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.38%

Overall 1.99% 32,160/1,614,012 alleles · low-frequency exomes 29,900/1,461,666 · genomes 2,260/152,346 · joint denominator

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	3.29%	30
Finnishnot grpmax-eligible	2.63%	38
European (non-Finnish)grpmax	2.42%	41
Remaining individualsnot grpmax-eligible	1.54%	65
Admixed American	0.735%	136
Ashkenazi Jewishnot grpmax-eligible	0.419%	239
African / African-American	0.401%	249
South Asian	0.0955%	1,047
Middle Eastern	0.0825%	1,212
East Asian	0.00223%	44,884

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Arg510=
Coding: c.1530C>T
MANE Select: NM_178554
dbSNP: rs35316983
Type: single nucleotide variant
Location: chr3:134604035 (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-arg510 (accessed [today's date]).

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