Is NEB p.Ser1652Pro (c.4954T>C) pathogenic?

NEB p.Ser1652Pro (c.4954T>C) is classified Likely benign in NEB (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-18). AlphaMissense: likely benign (0.0485); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with NEB p.Ser1652Pro (c.4954T>C)?

NEB p.Ser1652Pro (c.4954T>C) is associated with Inborn genetic diseases (ClinVar).

How common is NEB p.Ser1652Pro (c.4954T>C) in the general population?

NEB p.Ser1652Pro (c.4954T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about NEB p.Ser1652Pro (c.4954T>C)?

AlphaMissense predicts likely benign (score 0.0485) — an in-silico prediction, not a clinical call.

NEB p.Ser1652Pro

c.4954T>C · VCV3918523

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0485 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0485	likely benign
REVEL	0.047	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 4.6	GERP -1.4, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 82 kb · p 0.26 · regional, not allelic
Overall
CADD	11.65	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

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: NEB
Protein: p.Ser1652Pro
Coding: c.4954T>C
MANE Select: NM_001164508
Type: single nucleotide variant
Location: chr2:151666167 (GRCh38)
Gene constraint: LOEUF 0.597 · pLI <0.01 (gnomAD)
Residue 1652: a UniProt-annotated variant site (in amc6)

Full NEB 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

NEB p.Ser1652= Likely benign ★ same residue
NEB c.5344-1G>C Likely pathogenic ★★ same condition
NEB p.Ala1070Val Uncertain significance ★★ ⚠ same condition
NEB p.Ala1807Ser Uncertain significance ★★ ⚠ same condition
NEB p.Ala1823Ser Uncertain significance ★★ ⚠ same condition
NEB p.Ala1906Val Uncertain significance ★★ ⚠ same condition
NEB p.Ala251Pro Uncertain significance ★★ ⚠ same condition
NEB p.Ala2541Thr 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/neb-p-ser1652pro (accessed [today's date]).

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