Is PCNT p.Arg899His (c.2696G>A) pathogenic?

PCNT p.Arg899His (c.2696G>A) is classified Likely benign in PCNT (ClinVar, Single submitter, 2 submitters; last evaluated 2025-06-03). AlphaMissense: likely benign (0.0708); Ultra-rare (popmax 0.016%, afr); Associated with Inborn genetic diseases.

What condition is associated with PCNT p.Arg899His (c.2696G>A)?

PCNT p.Arg899His (c.2696G>A) is associated with Inborn genetic diseases (ClinVar).

How common is PCNT p.Arg899His (c.2696G>A) in the general population?

PCNT p.Arg899His (c.2696G>A) is ultra-rare (popmax 0.016%, afr) (gnomAD).

What do computational predictors say about PCNT p.Arg899His (c.2696G>A)?

AlphaMissense predicts likely benign (score 0.0708) — an in-silico prediction, not a clinical call.

PCNT p.Arg899His

c.2696G>A · rs549172396 · VCV2634233

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0708 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.016%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0708	likely benign
REVEL	0.025	moderately benign-leaning
SaProt	—	not scored · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.5	GERP -5.9
Regional constraint	o/e 1.03	unconstrained · MANE · 121 kb · p 0.027 · regional, not allelic
Overall
CADD	0.288	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.016% African / African-American · 12/75,040 alleles

Filtering AF 0.0092% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00721%

Overall 0.00211% 34/1,613,850 alleles · ultra-rare exomes 26/1,461,592 · genomes 8/152,258 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.016%	6,253
South Asian	0.0022%	45,538
Admixed American	0.00167%	60,012
Remaining individualsnot grpmax-eligible	0.0016%	62,504
European (non-Finnish)	0.00153%	65,554

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: PCNT
Protein: p.Arg899His
Coding: c.2696G>A
MANE Select: NM_006031
dbSNP: rs549172396
Type: single nucleotide variant
Location: chr21:46366670 (GRCh38)
Gene constraint: LOEUF 0.943 · pLI <0.01 (gnomAD)

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PCNT p.Arg899Cys Uncertain significance ★ ⚠ same residue
PCNT p.Arg899= Likely benign ★ same residue
PCNT p.Gln910Ter Pathogenic ★★ same condition
PCNT p.Ala1194Val Uncertain significance ★★ ⚠ same condition
PCNT p.Ala1400Thr Uncertain significance ★★ ⚠ same condition
PCNT p.Ala1457Val Uncertain significance ★★ ⚠ same condition
PCNT p.Ala1827Ser Uncertain significance ★★ ⚠ same condition
PCNT p.Ala1827Thr Uncertain significance ★★ ⚠ same condition

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/pcnt-p-arg899his (accessed [today's date]).

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