Is HPD p.Asn241Ser (c.722A>G) pathogenic?

HPD p.Asn241Ser (c.722A>G) is classified Pathogenic in HPD (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-11-08). AlphaMissense: likely pathogenic (0.5767); Very rare (popmax 0.000657%); Associated with hawkinsinuria.

What condition is associated with HPD p.Asn241Ser (c.722A>G)?

HPD p.Asn241Ser (c.722A>G) is associated with hawkinsinuria (ClinVar).

How common is HPD p.Asn241Ser (c.722A>G) in the general population?

HPD p.Asn241Ser (c.722A>G) is very rare (popmax 0.000657%) (gnomAD).

How is Hawkinsinuria inherited?

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

What do computational predictors say about HPD p.Asn241Ser (c.722A>G)?

AlphaMissense predicts likely pathogenic (score 0.5767) — an in-silico prediction, not a clinical call.

HPD p.Asn241Ser

c.722A>G · rs1276998235 · VCV979166

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5767 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000657%)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

hawkinsinuria

Computational evidence

Protein change
AlphaMissense	0.5767	likely pathogenic ✓ concordant with ClinVar
REVEL	0.601	indeterminate
SaProt	LLR -13.71	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.1	GERP 1.7, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 19 kb · p 0.004 · regional, not allelic
Overall
CADD	26.3	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

Grpmax group 0.000657%

Overall 0.000657% 1/152,162 alleles · very rare

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: HPD
Protein: p.Asn241Ser
Coding: c.722A>G
MANE Select: NM_002150
dbSNP: rs1276998235
Type: single nucleotide variant
Location: chr12:121847089 (GRCh38)
Gene constraint: LOEUF 0.845 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.00 · 4 PDB
Residue 241: a UniProt-annotated variant site (in tyrsn3; likely pathogenic); a UniProt-annotated variant site (in hwks; likely pathogenic; the orthologous rat mutation results in altered 4-hydroxyphenylpyruvate dioxygenase activity and accumulation of quinolacetic acid); the voc 2 domain; a β-strand

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

Disease context

hawkinsinuria — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Hawkinsinuria (Orphanet):

Inheritance: Autosomal dominant
Onset: Infancy, Neonatal
Prevalence: <1 / 1 000 000 (Worldwide)

Similar variants

HPD p.Arg225Ter Pathogenic/Likely pathogenic ★★ same condition
HPD p.Gln205Ter Pathogenic/Likely pathogenic ★★ same condition
HPD p.Tyr160Cys Likely pathogenic ★★ same condition
HPD p.Ala230Thr Uncertain significance ★★ ⚠ same condition
HPD p.Arg111Trp Uncertain significance ★★ ⚠ same condition
HPD p.Arg119Gln Uncertain significance ★★ ⚠ same condition
HPD p.Arg279Gly Uncertain significance ★★ ⚠ same condition
HPD p.Arg300Trp 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/hpd-p-asn241ser (accessed [today's date]).

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