Is PHEX p.Asp448fs (c.1344del) pathogenic?

PHEX p.Asp448fs (c.1344del) is classified Pathogenic in PHEX (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-12). No gnomAD frequency available for this variant.

How common is PHEX p.Asp448fs (c.1344del) in the general population?

PHEX p.Asp448fs (c.1344del) is no gnomAD frequency available for this variant (gnomAD).

PHEX p.Asp448fs

c.1344del · rs2518548157 · VCV2792492

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 12 of 22
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.4, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PHEX
Protein: p.Asp448fs
Coding: c.1344del
MANE Select: NM_000444
dbSNP: rs2518548157
Type: Deletion
Location: chrX:22133564 (GRCh38)
Structure: AlphaFold pLDDT 94.58
Residue 448: the peptidase m13 domain

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

Similar variants

PHEX p.Asp448= Conflicting classifications of pathogenicity ★ same residue
PHEX c.1079+2_1079+5del Pathogenic ★★ same type
PHEX c.187+1del Pathogenic ★★ same type
PHEX c.2147+2_2147+9del Pathogenic ★★ same type
PHEX p.Ala242fs Pathogenic ★★ same type
PHEX p.Ala295fs Pathogenic ★★ same type
PHEX p.Ala730fs Pathogenic ★★ same type
PHEX p.Asn723_Phe724insTer 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/phex-p-asp448fs (accessed [today's date]).

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