Is PHEX p.Val179= (c.537T>A) pathogenic?

PHEX p.Val179= (c.537T>A) is classified Benign/Likely benign in PHEX (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-26). Low-frequency (popmax 2.28%, afr); Associated with X-linked dominant hypophosphatemic rickets.

What condition is associated with PHEX p.Val179= (c.537T>A)?

PHEX p.Val179= (c.537T>A) is associated with X-linked dominant hypophosphatemic rickets (ClinVar).

How common is PHEX p.Val179= (c.537T>A) in the general population?

PHEX p.Val179= (c.537T>A) is low-frequency (popmax 2.28%, afr) (gnomAD).

How is X-linked hypophosphatemia inherited?

Typically X-linked dominant (Orphanet). A genetic counselor can assess individual risk for a family.

PHEX p.Val179=

c.537T>A · rs137961493 · VCV368162

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

low-frequency (popmax 2.28%, afr)

Conditions

X-linked dominant hypophosphatemic rickets

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1	GERP -1, phastCons 1
Overall
CADD	9.532	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 2.28% African / African-American · 1,305/57,233 alleles

Filtering AF 2.18% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.14%

Overall 0.126% 1,521/1,209,552 alleles · low-frequency exomes 760/1,097,557 · genomes 761/111,995 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.28%	44
Remaining individualsnot grpmax-eligible	0.2%	501
Admixed American	0.192%	520
Middle Eastern	0.0919%	1,089
South Asian	0.00528%	18,937
European (non-Finnish)	0.00291%	34,412

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: PHEX
Protein: p.Val179=
Coding: c.537T>A
MANE Select: NM_000444
dbSNP: rs137961493
Type: single nucleotide variant
Location: chrX:22077576 (GRCh38)
Structure: AlphaFold pLDDT 94.58
Residue 179: the peptidase m13 domain

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

Disease context

X-linked dominant hypophosphatemic rickets — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For X-linked hypophosphatemia (Orphanet):

Inheritance: X-linked dominant
Onset: Childhood, Infancy
Prevalence: 1-9 / 100 000 (Norway)

Similar variants

PHEX p.Val179fs Pathogenic ★ same residue
PHEX c.1079+1G>A Pathogenic ★★ same condition
PHEX c.1079+2T>G Pathogenic ★★ same condition
PHEX c.1080-1G>A Pathogenic ★★ same condition
PHEX c.1080-3C>G Pathogenic ★★ same condition
PHEX c.1173+1G>A Pathogenic ★★ same condition
PHEX c.1173+5G>C Likely pathogenic ★★ same condition
PHEX c.1174-1G>A Pathogenic ★★ 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/phex-p-val179 (accessed [today's date]).

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