Is NPC1 p.Ser849Ile (c.2546G>T) pathogenic?

NPC1 p.Ser849Ile (c.2546G>T) is classified Likely pathogenic in NPC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-05-01). AlphaMissense: likely pathogenic (0.9126); Absent from gnomAD v4.1.

How common is NPC1 p.Ser849Ile (c.2546G>T) in the general population?

NPC1 p.Ser849Ile (c.2546G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about NPC1 p.Ser849Ile (c.2546G>T)?

AlphaMissense predicts likely pathogenic (score 0.9126) — an in-silico prediction, not a clinical call.

NPC1 p.Ser849Ile

c.2546G>T · rs1057519242 · VCV374777

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9126 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9126	likely pathogenic ✓ concordant with ClinVar
REVEL	0.938	strongly pathogenic-leaning
SaProt	LLR -17.31	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.8	GERP 0.99, phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 54 kb · p 0.0029 · regional, not allelic
Overall
CADD	26.4	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: NPC1
Protein: p.Ser849Ile
Coding: c.2546G>T
MANE Select: NM_000271
dbSNP: rs1057519242
Type: single nucleotide variant
Location: chr18:23540506 (GRCh38)
Gene constraint: LOEUF 0.676 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.35 · 20 PDB
Residue 849: a UniProt-annotated variant site (in npc1); an α-helix

Full NPC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

NPC1 c.1554-1009G>A Pathogenic ★★ same type
NPC1 c.1757+1G>A Likely pathogenic ★★ same type
NPC1 c.1947+5G>C Pathogenic/Likely pathogenic ★★ same type
NPC1 c.2130+1G>A Pathogenic ★★ same type
NPC1 c.2245+1G>A Pathogenic/Likely pathogenic ★★ same type
NPC1 c.2246-2A>G Pathogenic/Likely pathogenic ★★ same type
NPC1 c.2515-2A>G Pathogenic/Likely pathogenic ★★ same type
NPC1 c.2604+1G>A Pathogenic/Likely pathogenic ★★ same type

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/npc1-p-ser849ile (accessed [today's date]).

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