Is NFIX p.Phe137Ser (c.410T>C) pathogenic?

NFIX p.Phe137Ser (c.410T>C) is classified Uncertain significance in NFIX (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-07). AlphaMissense: likely pathogenic (0.9991); Absent from gnomAD v4.1.

How common is NFIX p.Phe137Ser (c.410T>C) in the general population?

NFIX p.Phe137Ser (c.410T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about NFIX p.Phe137Ser (c.410T>C)?

AlphaMissense predicts likely pathogenic (score 0.9991) — an in-silico prediction, not a clinical call.

NFIX p.Phe137Ser

c.410T>C · rs2512746375 · VCV1708760

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9991 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9991	likely pathogenic · top 5% in NFIX
REVEL	0.905	moderately pathogenic-leaning
SaProt	LLR -16.98	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 8	GERP 2.8, phastCons 1
Regional constraint	o/e 0.05	constrained · MANE · 128 bp · p 6.8e-13 · regional, not allelic
Overall
CADD	33.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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: NFIX
Protein: p.Phe137Ser
Coding: c.410T>C
MANE Select: NM_001365902
dbSNP: rs2512746375
Type: single nucleotide variant
Location: chr19:13025403 (GRCh38)
Gene constraint: LOEUF 0.092 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 62.94 · 3 PDB
Residue 137: a DNA-binding region; an α-helix

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

Similar variants

NFIX p.Phe137Cys Likely pathogenic ★ same residue
NFIX c.559+1G>A Pathogenic ★★ same type
NFIX c.697+1G>A Pathogenic/Likely pathogenic ★★ same type
NFIX c.818+1G>A Likely pathogenic ★★ same type
NFIX c.955+1G>A Pathogenic ★★ same type
NFIX c.955+1G>T Pathogenic ★★ same type
NFIX p.Arg115Gln Pathogenic/Likely pathogenic ★★ same type
NFIX p.Arg116Gln 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/nfix-p-phe137ser (accessed [today's date]).

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